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Jomova K, Makova M, Alomar SY, Alwasel SH, Nepovimova E, Kuca K, Rhodes CJ, Valko M. Essential metals in health and disease. Chem Biol Interact 2022; 367:110173. [PMID: 36152810 DOI: 10.1016/j.cbi.2022.110173] [Citation(s) in RCA: 159] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/10/2022] [Accepted: 09/05/2022] [Indexed: 11/03/2022]
Abstract
In total, twenty elements appear to be essential for the correct functioning of the human body, half of which are metals and half are non-metals. Among those metals that are currently considered to be essential for normal biological functioning are four main group elements, sodium (Na), potassium (K), magnesium (Mg), and calcium (Ca), and six d-block transition metal elements, manganese (Mn), iron (Fe), cobalt (Co), copper (Cu), zinc (Zn) and molybdenum (Mo). Cells have developed various metallo-regulatory mechanisms for maintaining a necessary homeostasis of metal-ions for diverse cellular processes, most importantly in the central nervous system. Since redox active transition metals (for example Fe and Cu) may participate in electron transfer reactions, their homeostasis must be carefully controlled. The catalytic behaviour of redox metals which have escaped control, e.g. via the Fenton reaction, results in the formation of reactive hydroxyl radicals, which may cause damage to DNA, proteins and membranes. Transition metals are integral parts of the active centers of numerous enzymes (e.g. Cu,Zn-SOD, Mn-SOD, Catalase) which catalyze chemical reactions at physiologically compatible rates. Either a deficiency, or an excess of essential metals may result in various disease states arising in an organism. Some typical ailments that are characterized by a disturbed homeostasis of redox active metals include neurological disorders (Alzheimer's, Parkinson's and Huntington's disorders), mental health problems, cardiovascular diseases, cancer, and diabetes. To comprehend more deeply the mechanisms by which essential metals, acting either alone or in combination, and/or through their interaction with non-essential metals (e.g. chromium) function in biological systems will require the application of a broader, more interdisciplinary approach than has mainly been used so far. It is clear that a stronger cooperation between bioinorganic chemists and biophysicists - who have already achieved great success in understanding the structure and role of metalloenzymes in living systems - with biologists, will access new avenues of research in the systems biology of metal ions. With this in mind, the present paper reviews selected chemical and biological aspects of metal ions and their possible interactions in living systems under normal and pathological conditions.
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Affiliation(s)
- Klaudia Jomova
- Department of Chemistry, Faculty of Natural Sciences and Informatics, Constantine The Philosopher University in Nitra, 949 01, Nitra, Slovakia
| | - Marianna Makova
- Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, 812 37, Bratislava, Slovakia
| | - Suliman Y Alomar
- King Saud University, Zoology Department, College of Science, Riyadh, 11451, Saudi Arabia
| | - Saleh H Alwasel
- King Saud University, Zoology Department, College of Science, Riyadh, 11451, Saudi Arabia
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | | | - Marian Valko
- Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, 812 37, Bratislava, Slovakia; King Saud University, Zoology Department, College of Science, Riyadh, 11451, Saudi Arabia.
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2
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Yaduvanshi S, Ero R, Kumar V. The mechanism of complex formation between calmodulin and voltage gated calcium channels revealed by molecular dynamics. PLoS One 2021; 16:e0258112. [PMID: 34610038 PMCID: PMC8491939 DOI: 10.1371/journal.pone.0258112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/18/2021] [Indexed: 11/18/2022] Open
Abstract
Calmodulin, a ubiquitous eukaryotic calcium sensor responsible for the regulation of many fundamental cellular processes, is a highly flexible protein and exhibits an unusually wide range of conformations. Furthermore, CaM is known to interact with more than 300 cellular targets. Molecular dynamics (MD) simulation trajectories suggest that EF-hand loops show different magnitudes of flexibility. Therefore, the four EF-hand motifs have different affinities for Ca2+ ions, which enables CaM to function on wide range of Ca2+ ion concentrations. EF-hand loops are 2-3 times more flexible in apo CaM whereas least flexible in Ca2+/CaM-IQ motif complexes. We report a unique intermediate conformation of Ca2+/CaM while transitioning from extended to compact form. We also report the complex formation process between Ca2+/CaM and IQ CaM-binding motifs. Our results showed how IQ motif recognise its binding site on the CaM and how CaM transforms from extended to compact form upon binding to IQ motif.
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Affiliation(s)
- Shivani Yaduvanshi
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Noida, Noida, Uttar Pradesh, India
| | - Rya Ero
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Veerendra Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Noida, Noida, Uttar Pradesh, India
- * E-mail:
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3
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Rayani K, Seffernick J, Li AY, Davis JP, Spuches AM, Van Petegem F, Solaro RJ, Lindert S, Tibbits GF. Binding of calcium and magnesium to human cardiac troponin C. J Biol Chem 2021; 296:100350. [PMID: 33548225 PMCID: PMC7961095 DOI: 10.1016/j.jbc.2021.100350] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
Cardiac muscle thin filaments are composed of actin, tropomyosin, and troponin that change conformation in response to Ca2+ binding, triggering muscle contraction. Human cardiac troponin C (cTnC) is the Ca2+-sensing component of the thin filament. It contains structural sites (III/IV) that bind both Ca2+ and Mg2+ and a regulatory site (II) that has been thought to bind only Ca2+. Binding of Ca2+ at this site initiates a series of conformational changes that culminate in force production. However, the mechanisms that underpin the regulation of binding at site II remain unclear. Here, we have quantified the interaction between site II and Ca2+/Mg2+ through isothermal titration calorimetry and thermodynamic integration simulations. Direct and competitive binding titrations with WT N-terminal cTnC and full-length cTnC indicate that physiologically relevant concentrations of both Ca2+/Mg2+ interacted with the same locus. Moreover, the D67A/D73A N-terminal cTnC construct in which two coordinating residues within site II were removed was found to have significantly reduced affinity for both cations. In addition, 1 mM Mg2+ caused a 1.4-fold lower affinity for Ca2+. These experiments strongly suggest that cytosolic-free Mg2+ occupies a significant population of the available site II. Interaction of Mg2+ with site II of cTnC likely has important functional consequences for the heart both at baseline as well as in diseased states that decrease or increase the availability of Mg2+, such as secondary hyperparathyroidism or ischemia, respectively.
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Affiliation(s)
- Kaveh Rayani
- Molecular Cardiac Physiology Group, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Justin Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio, USA
| | - Alison Yueh Li
- Molecular Cardiac Physiology Group, Simon Fraser University, Burnaby, British Columbia, Canada; Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jonathan P Davis
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio, USA
| | - Anne Marie Spuches
- Department of Chemistry, East Carolina University, 300 Science and Technology Building, Greenville, North Carolina, USA
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - R John Solaro
- Department of Physiology and Biophysics and the Center for Cardiovascular Research, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio, USA
| | - Glen F Tibbits
- Molecular Cardiac Physiology Group, Simon Fraser University, Burnaby, British Columbia, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Cardiac Group, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.
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Intrinsically disordered protein domain of human ameloblastin in synthetic fusion with calmodulin increases calmodulin stability and modulates its function. Int J Biol Macromol 2020; 168:1-12. [PMID: 33290768 DOI: 10.1016/j.ijbiomac.2020.11.216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 11/21/2022]
Abstract
Constantly increasing attention to bioengineered proteins has led to the rapid development of new functional targets. Here we present the biophysical and functional characteristics of the newly designed CaM/AMBN-Ct fusion protein. The two-domain artificial target consists of calmodulin (CaM) and ameloblastin C-terminus (AMBN-Ct). CaM as a well-characterized calcium ions (Ca2+) binding protein offers plenty of options in terms of Ca2+ detection in biomedicine and biotechnologies. Highly negatively charged AMBN-Ct belongs to intrinsically disordered proteins (IDPs). CaM/AMBN-Ct was designed to open new ways of communication synergies between the domains with potential functional improvement. The character and function of CaM/AMBN-Ct were explored by biophysical and molecular modelling methods. Experimental studies have revealed increased stability and preserved CaM/AMBN-Ct function. The results of molecular dynamic simulations (MDs) outlined different interface patterns between the domains with potential allosteric communication within the fusion.
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Bombardi L, Pedretti M, Conter C, Dominici P, Astegno A. Distinct Calcium Binding and Structural Properties of Two Centrin Isoforms from Toxoplasma gondii. Biomolecules 2020; 10:E1142. [PMID: 32759683 PMCID: PMC7465447 DOI: 10.3390/biom10081142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 11/16/2022] Open
Abstract
Centrins are calcium (Ca2+)-binding proteins that have been implicated in several regulatory functions. In the protozoan parasite Toxoplasma gondii, the causative agent of toxoplasmosis, three isoforms of centrin have been identified. While increasing information is now available that links the function of centrins with defined parasite biological processes, knowledge is still limited on the metal-binding and structural properties of these proteins. Herein, using biophysical and structural approaches, we explored the Ca2+ binding abilities and the subsequent effects of Ca2+ on the structure of a conserved (TgCEN1) and a more divergent (TgCEN2) centrin isoform from T. gondii. Our data showed that TgCEN1 and TgCEN2 possess diverse molecular features, suggesting that they play nonredundant roles in parasite physiology. TgCEN1 binds two Ca2+ ions with high/medium affinity, while TgCEN2 binds one Ca2+ with low affinity. TgCEN1 undergoes significant Ca2+-dependent conformational changes that expose hydrophobic patches, supporting a role as a Ca2+ sensor in toxoplasma. In contrast, Ca2+ binding has a subtle influence on conformational features of TgCEN2 without resulting in hydrophobic exposure, suggesting a different Ca2+ relay mode for this isoform. Furthermore, TgCEN1 displays a Ca2+-dependent ability to self-assemble, while TgCEN2 did not. We discuss our findings in the context of Ca2+ signaling in toxoplasma.
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Affiliation(s)
| | | | | | | | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (L.B.); (M.P.); (C.C.); (P.D.)
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6
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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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7
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Niu J, Dick IE, Yang W, Bamgboye MA, Yue DT, Tomaselli G, Inoue T, Ben-Johny M. Allosteric regulators selectively prevent Ca 2+-feedback of Ca V and Na V channels. eLife 2018; 7:35222. [PMID: 30198845 PMCID: PMC6156082 DOI: 10.7554/elife.35222] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 09/09/2018] [Indexed: 12/31/2022] Open
Abstract
Calmodulin (CaM) serves as a pervasive regulatory subunit of CaV1, CaV2, and NaV1 channels, exploiting a functionally conserved carboxy-tail element to afford dynamic Ca2+-feedback of cellular excitability in neurons and cardiomyocytes. Yet this modularity counters functional adaptability, as global changes in ambient CaM indiscriminately alter its targets. Here, we demonstrate that two structurally unrelated proteins, SH3 and cysteine-rich domain (stac) and fibroblast growth factor homologous factors (fhf) selectively diminish Ca2+/CaM-regulation of CaV1 and NaV1 families, respectively. The two proteins operate on allosteric sites within upstream portions of respective channel carboxy-tails, distinct from the CaM-binding interface. Generalizing this mechanism, insertion of a short RxxK binding motif into CaV1.3 carboxy-tail confers synthetic switching of CaM regulation by Mona SH3 domain. Overall, our findings identify a general class of auxiliary proteins that modify Ca2+/CaM signaling to individual targets allowing spatial and temporal orchestration of feedback, and outline strategies for engineering Ca2+/CaM signaling to individual targets.
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Affiliation(s)
- Jacqueline Niu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, United States
| | - Ivy E Dick
- Department of Physiology, University of Maryland, Baltimore, United States
| | - Wanjun Yang
- Department of Cardiology, Johns Hopkins University, Baltimore, United States
| | | | - David T Yue
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, United States
| | - Gordon Tomaselli
- Department of Cardiology, Johns Hopkins University, Baltimore, United States
| | - Takanari Inoue
- Department of Cell Biology, Johns Hopkins University, Baltimore, United States.,Center for Cell Dynamics, Institute for Basic Biomedical Sciences, Johns Hopkins University, Baltimore, United States
| | - Manu Ben-Johny
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, United States
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8
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Structural dynamics of calmodulin-ryanodine receptor interactions: electron paramagnetic resonance using stereospecific spin labels. Sci Rep 2018; 8:10681. [PMID: 30013092 PMCID: PMC6048129 DOI: 10.1038/s41598-018-29064-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/27/2018] [Indexed: 12/30/2022] Open
Abstract
We have used electron paramagnetic resonance, with rigid and stereospecific spin labels, to resolve structural states in calmodulin (CaM), as affected by binding of Ca and a CaM-binding peptide (RyRp) derived from the ryanodine receptor (RyR), the Ca channel that triggers muscle contraction. CaM mutants containing a pair of cysteines in the N-lobe and/or C-lobe were engineered and labeled with a stereospecifically bound bifunctional spin label (BSL). RyRp was synthesized with and without TOAC (a stereospecifically attached spin-labeled amino acid) substituted for a single amino acid near the N-terminus. Intramolecular DEER distance measurements of doubly-labeled BSL-CaM revealed that CaM exists in dynamic equilibrium among multiple states, consistent with open, closed, and compact structural models. Addition of RyRp shifted the equilibrium partially toward the compact state in the absence of Ca, and completely toward the compact state in the presence of Ca, supporting a conformational selection model. Inter-protein distance measurements show that Ca stabilizes the compact state primarily by inducing ordered binding of the CaM N-lobe to RyRp, while only slightly affecting the C-lobe. The results provide insight into the structural mechanism of CaM-mediated RyR regulation, while demonstrating the power of using two types of rigidly and stereospecifically bound spin labels.
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Brown KL, Banerjee S, Feigley A, Abe H, Blackwell TS, Pozzi A, Hudson BG, Zent R. Salt-bridge modulates differential calcium-mediated ligand binding to integrin α1- and α2-I domains. Sci Rep 2018; 8:2916. [PMID: 29440721 PMCID: PMC5811549 DOI: 10.1038/s41598-018-21231-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/31/2018] [Indexed: 11/11/2022] Open
Abstract
Integrins are transmembrane cell-extracellular matrix adhesion receptors that impact many cellular functions. A subgroup of integrins contain an inserted (I) domain within the α–subunits (αI) that mediate ligand recognition where function is contingent on binding a divalent cation at the metal ion dependent adhesion site (MIDAS). Ca2+ is reported to promote α1I but inhibit α2I ligand binding. We co-crystallized individual I-domains with MIDAS-bound Ca2+ and report structures at 1.4 and 2.15 Å resolution, respectively. Both structures are in the “closed” ligand binding conformation where Ca2+ induces minimal global structural changes. Comparisons with Mg2+-bound structures reveal Mg2+ and Ca2+ bind α1I in a manner sufficient to promote ligand binding. In contrast, Ca2+ is displaced in the α2I domain MIDAS by 1.4 Å relative to Mg2+ and unable to directly coordinate all MIDAS residues. We identified an E152-R192 salt bridge hypothesized to limit the flexibility of the α2I MIDAS, thus, reducing Ca2+ binding. A α2I E152A construct resulted in a 10,000-fold increase in Mg2+ and Ca2+ binding affinity while increasing binding to collagen ligands 20%. These data indicate the E152-R192 salt bridge is a key distinction in the molecular mechanism of differential ion binding of these two I domains.
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Affiliation(s)
- Kyle L Brown
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. .,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. .,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.
| | - Surajit Banerjee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.,Northeastern Collaborative Access Team, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Andrew Feigley
- Leadership Alliance, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA
| | - Hanna Abe
- Aspirnaut Summer research program, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA
| | - Timothy S Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Veterans Affairs Hospital, Nashville, TN, 37232, USA
| | - Ambra Pozzi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Veterans Affairs Hospital, Nashville, TN, 37232, USA
| | - Billy G Hudson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Aspirnaut Summer research program, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232-2372, USA
| | - Roy Zent
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Veterans Affairs Hospital, Nashville, TN, 37232, USA
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Green JL, Wall RJ, Vahokoski J, Yusuf NA, Ridzuan MAM, Stanway RR, Stock J, Knuepfer E, Brady D, Martin SR, Howell SA, Pires IP, Moon RW, Molloy JE, Kursula I, Tewari R, Holder AA. Compositional and expression analyses of the glideosome during the Plasmodium life cycle reveal an additional myosin light chain required for maximum motility. J Biol Chem 2017; 292:17857-17875. [PMID: 28893907 PMCID: PMC5663884 DOI: 10.1074/jbc.m117.802769] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/04/2017] [Indexed: 11/06/2022] Open
Abstract
Myosin A (MyoA) is a Class XIV myosin implicated in gliding motility and host cell and tissue invasion by malaria parasites. MyoA is part of a membrane-associated protein complex called the glideosome, which is essential for parasite motility and includes the MyoA light chain myosin tail domain-interacting protein (MTIP) and several glideosome-associated proteins (GAPs). However, most studies of MyoA have focused on single stages of the parasite life cycle. We examined MyoA expression throughout the Plasmodium berghei life cycle in both mammalian and insect hosts. In extracellular ookinetes, sporozoites, and merozoites, MyoA was located at the parasite periphery. In the sexual stages, zygote formation and initial ookinete differentiation precede MyoA synthesis and deposition, which occurred only in the developing protuberance. In developing intracellular asexual blood stages, MyoA was synthesized in mature schizonts and was located at the periphery of segmenting merozoites, where it remained throughout maturation, merozoite egress, and host cell invasion. Besides the known GAPs in the malaria parasite, the complex included GAP40, an additional myosin light chain designated essential light chain (ELC), and several other candidate components. This ELC bound the MyoA neck region adjacent to the MTIP-binding site, and both myosin light chains co-located to the glideosome. Co-expression of MyoA with its two light chains revealed that the presence of both light chains enhances MyoA-dependent actin motility. In conclusion, we have established a system to study the interplay and function of the three glideosome components, enabling the assessment of inhibitors that target this motor complex to block host cell invasion.
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Affiliation(s)
| | - Richard J Wall
- the School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | - Juha Vahokoski
- the Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | | | | | - Rebecca R Stanway
- the Institute of Cell Biology, University of Bern, Bern, Switzerland, and
| | - Jessica Stock
- the School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | | | - Declan Brady
- the School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | | | | | - Isa P Pires
- the Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | | | - Justin E Molloy
- Single Molecule Enzymology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom
| | - Inari Kursula
- the Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.,the Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Rita Tewari
- the School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom
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Molecular Basis for Modulation of Metabotropic Glutamate Receptors and Their Drug Actions by Extracellular Ca 2. Int J Mol Sci 2017; 18:ijms18030672. [PMID: 28335551 PMCID: PMC5372683 DOI: 10.3390/ijms18030672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/13/2017] [Accepted: 03/17/2017] [Indexed: 12/24/2022] Open
Abstract
Metabotropic glutamate receptors (mGluRs) associated with the slow phase of the glutamatergic signaling pathway in neurons of the central nervous system have gained importance as drug targets for chronic neurodegenerative diseases. While extracellular Ca2+ was reported to exhibit direct activation and modulation via an allosteric site, the identification of those binding sites was challenged by weak binding. Herein, we review the discovery of extracellular Ca2+ in regulation of mGluRs, summarize the recent developments in probing Ca2+ binding and its co-regulation of the receptor based on structural and biochemical analysis, and discuss the molecular basis for Ca2+ to regulate various classes of drug action as well as its importance as an allosteric modulator in mGluRs.
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12
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Walton SD, Chakravarthy H, Shettigar V, O’Neil AJ, Siddiqui JK, Jones BR, Tikunova SB, Davis JP. Divergent Soybean Calmodulins Respond Similarly to Calcium Transients: Insight into Differential Target Regulation. FRONTIERS IN PLANT SCIENCE 2017; 8:208. [PMID: 28261258 PMCID: PMC5309217 DOI: 10.3389/fpls.2017.00208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/03/2017] [Indexed: 05/07/2023]
Abstract
Plants commonly respond to stressors by modulating the expression of a large family of calcium binding proteins including isoforms of the ubiquitous signaling protein calmodulin (CaM). The various plant CaM isoforms are thought to differentially regulate the activity of specific target proteins to modulate cellular stress responses. The mechanism(s) behind differential target activation by the plant CaMs is unknown. In this study, we used steady-state and stopped-flow fluorescence spectroscopy to investigate the strategy by which two soybean CaMs (sCaM1 and sCaM4) have evolved to differentially regulate NAD kinase (NADK), which is activated by sCaM1 but inhibited by sCaM4. Although the isolated proteins have different cation binding properties, in the presence of Mg2+ and the CaM binding domains from proteins that are differentially regulated, the two plant CaMs respond nearly identically to rapid and slow Ca2+ transients. Our data suggest that the plant CaMs have evolved to bind certain targets with comparable affinities, respond similarly to a particular Ca2+ signature, but achieve different structural states, only one of which can activate the enzyme. Understanding the basis for differential enzyme regulation by the plant CaMs is the first step to engineering a vertebrate CaM that will selectively alter the CaM signaling network.
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Affiliation(s)
| | | | | | | | | | | | | | - Jonathan P. Davis
- Department of Physiology and Cell Biology, The Ohio State UniversityColumbus, OH, USA
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13
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Debold EP. Decreased Myofilament Calcium Sensitivity Plays a Significant Role in Muscle Fatigue. Exerc Sport Sci Rev 2016; 44:144-9. [DOI: 10.1249/jes.0000000000000089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Designing proteins to combat disease: Cardiac troponin C as an example. Arch Biochem Biophys 2016; 601:4-10. [PMID: 26901433 DOI: 10.1016/j.abb.2016.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/04/2016] [Indexed: 01/18/2023]
Abstract
Throughout history, muscle research has led to numerous scientific breakthroughs that have brought insight to a more general understanding of all biological processes. Potentially one of the most influential discoveries was the role of the second messenger calcium and its myriad of handling and sensing systems that mechanistically control muscle contraction. In this review we will briefly discuss the significance of calcium as a universal second messenger along with some of the most common calcium binding motifs in proteins, focusing on the EF-hand. We will also describe some of our approaches to rationally design calcium binding proteins to palliate, or potentially even cure cardiovascular disease. Considering not all failing hearts have the same etiology, genetic background and co-morbidities, personalized therapies will need to be developed. We predict designer proteins will open doors for unprecedented personalized, and potentially, even generalized medicines as gene therapy or protein delivery techniques come to fruition.
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15
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Dimerization of peptides by calcium ions: investigation of a calcium-binding motif. INTERNATIONAL JOURNAL OF PROTEOMICS 2014; 2014:153712. [PMID: 25295190 PMCID: PMC4177772 DOI: 10.1155/2014/153712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/11/2014] [Indexed: 12/28/2022]
Abstract
We investigated calcium-binding motifs of peptides and their recognition of active functionalities for coordination. This investigation generates the fundamentals to design carrier material for calcium-bound peptide-peptide interactions. Interactions of different peptides with active calcium domains were investigated. Evaluation of selectivity was performed by electrospray ionization mass spectrometry by infusing solutions containing two different peptides (P1 and P2) in the presence of calcium ions. In addition to signals for monomer species, intense dimer signals are observed for the heterodimer ions (P1 ⋯ Ca2+ ⋯ P2) (⋯ represents the noncovalent binding of calcium with the peptide) in the positive ion mode and for ions ([P1-2H]2− ⋯ Ca2+ ⋯ [P2-2H]2−) in the negative ion mode. Monitoring of the dissociation from these mass selected dimer ions via the kinetic method provides information on the calcium affinity order of different peptide sequences.
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16
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Conservation of Ca2+/calmodulin regulation across Na and Ca2+ channels. Cell 2014; 157:1657-70. [PMID: 24949975 DOI: 10.1016/j.cell.2014.04.035] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/25/2014] [Accepted: 04/15/2014] [Indexed: 11/20/2022]
Abstract
Voltage-gated Na and Ca2+ channels comprise distinct ion channel superfamilies, yet the carboxy tails of these channels exhibit high homology, hinting at a long-shared and purposeful module. For different Ca2+ channels, carboxyl-tail interactions with calmodulin do elaborate robust and similar forms of Ca2+ regulation. However, Na channels have only shown subtler Ca2+ modulation that differs among reports, challenging attempts at unified understanding. Here, by rapid Ca2+ photorelease onto Na channels, we reset this view of Na channel regulation. For cardiac-muscle channels (NaV1.5), reported effects from which most mechanistic proposals derive, we observe no Ca2+ modulation. Conversely, for skeletal-muscle channels (NaV1.4), we uncover fast Ca2+ regulation eerily similar to that of Ca2+ channels. Channelopathic myotonia mutations halve NaV1.4 Ca2+ regulation, and transplanting the NaV1.4 carboxy tail onto Ca2+ channels recapitulates Ca2+ regulation. Thus, we argue for the persistence and physiological relevance of an ancient Ca2+ regulatory module across Na and Ca2+ channels.
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17
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Mazumder M, Padhan N, Bhattacharya A, Gourinath S. Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity. PLoS One 2014; 9:e96202. [PMID: 24760183 PMCID: PMC3997525 DOI: 10.1371/journal.pone.0096202] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/04/2014] [Indexed: 12/31/2022] Open
Abstract
The diversity of functions carried out by EF hand-containing calcium-binding proteins is due to various interactions made by these proteins as well as the range of affinity levels for Ca2+ displayed by them. However, accurate methods are not available for prediction of binding affinities. Here, amino acid patterns of canonical EF hand sequences obtained from available crystal structures were used to develop a classifier that distinguishes Ca2+-binding loops and non Ca2+-binding regions with 100% accuracy. To investigate further, we performed a proteome-wide prediction for E. histolytica, and classified known EF-hand proteins. We compared our results with published methods on the E. histolytica proteome scan, and demonstrated our method to be more specific and accurate for predicting potential canonical Ca2+-binding loops. Furthermore, we annotated canonical EF-hand motifs and classified them based on their Ca2+-binding affinities using support vector machines. Using a novel method generated from position-specific scoring metrics and then tested against three different experimentally derived EF-hand-motif datasets, predictions of Ca2+-binding affinities were between 87 and 90% accurate. Our results show that the tool described here is capable of predicting Ca2+-binding affinity constants of EF-hand proteins. The web server is freely available at http://202.41.10.46/calb/index.html.
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Affiliation(s)
- Mohit Mazumder
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Narendra Padhan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- Department of Immunology, Genetics, and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Samudrala Gourinath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
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18
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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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19
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Mishra A, Suman SK, Srivastava SS, Sankaranarayanan R, Sharma Y. Decoding the molecular design principles underlying Ca(2+) binding to βγ-crystallin motifs. J Mol Biol 2011; 415:75-91. [PMID: 22099475 DOI: 10.1016/j.jmb.2011.10.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 10/19/2011] [Accepted: 10/20/2011] [Indexed: 11/19/2022]
Abstract
Numerous proteins belonging to the recently expanded βγ-crystallin superfamily bind Ca(2+) at the double-clamp N/D-N/D-X(1)-X(2)-S/T-S motif. However, there have been no attempts to understand the intricacies involving Ca(2+) binding, such as the determinants of Ca(2+)-binding affinity and their contributions to gain in stability. This work is an in-depth analysis of understanding the modes and determinants of Ca(2+) binding to βγ-crystallin motifs. We have performed extensive naturally occurring substitutions from related proteins on the βγ-crystallin domains of flavollin, a low-affinity Ca(2+)-binding protein, and clostrillin, a moderate-affinity protein. We monitored the consequences of these modifications on Ca(2)(+) binding by isothermal titration calorimetry, thermal stability and conformational and crystal structure analyses. We demonstrate that Ca(2)(+) binding to the two sites of a βγ-domain is interdependent and that the presence of Arg at the fifth position disables a site. A change from Thr to Ser, or vice versa, influences Ca(2+)-binding affinity, highlighting the basis of diversity found in these domains. A subtle change in the first site has a greater influence on Ca(2)(+) binding than a similar alteration in the second site. Thus, the second site is more variable in nature. Replacing an acidic or hydrophobic residue in a binding site alters the Ca(2+)-binding properties drastically. While it appears from their binding site sequence that these domains have evolved randomly, our examination illustrates the subtlety in the design of these modules. Decoding such design schemes would aid in our understanding of the functional themes underlying differential Ca(2)(+) binding and in predicting these in emerging sequence information.
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Affiliation(s)
- Amita Mishra
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad 500007, India
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20
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Chandra K, Mustafi SM, Muthukumar S, Chary KVR. Site-Specific Free Energy Changes in Proteins upon Ligand Binding by Nuclear Magnetic Resonance: Ca2+-Displacement by Ln3+ in a Ca2+-Binding Protein from Entamoeba histolytica. Chem Biol Drug Des 2011; 77:272-80. [DOI: 10.1111/j.1747-0285.2011.01090.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Abstract
Ca2+-ions have a range of affinities to different proteins, depending on the various functions of these proteins. This makes the determination of Ca2+-protein affinities an interesting subject for functional studies. We have investigated the performance of two methods – Fold-X and AutoDock vina – in the prediction of Ca2+-protein affinities. Both methods, although based on different energy functions, showed virtually the same correlation with experimental affinities. Guided by insight from experiment, we further derived a simple linear model based on the solvent accessible surface of Ca2+ that had practically the same performance in terms of absolute errors as the more complex docking methods.
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Affiliation(s)
- Stefan Franke
- Department of Bioinformatics/Centre for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
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22
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Zhou Y, Tzeng WP, Wong HC, Ye Y, Jiang J, Chen Y, Huang Y, Suppiah S, Frey TK, Yang JJ. Calcium-dependent association of calmodulin with the rubella virus nonstructural protease domain. J Biol Chem 2010; 285:8855-68. [PMID: 20086014 DOI: 10.1074/jbc.m109.097063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The rubella virus (RUBV) nonstructural (NS) protease domain, a Ca(2+)- and Zn(2+)-binding papain-like cysteine protease domain within the nonstructural replicase polyprotein precursor, is responsible for the self-cleavage of the precursor into two mature products, P150 and P90, that compose the replication complex that mediates viral RNA replication; the NS protease resides at the C terminus of P150. Here we report the Ca(2+)-dependent, stoichiometric association of calmodulin (CaM) with the RUBV NS protease. Co-immunoprecipitation and pulldown assays coupled with site-directed mutagenesis demonstrated that both the P150 protein and a 110-residue minidomain within NS protease interacted directly with Ca(2+)/CaM. The specific interaction was mapped to a putative CaM-binding domain. A 32-mer peptide (residues 1152-1183, denoted as RUBpep) containing the putative CaM-binding domain was used to investigate the association of RUBV NS protease with CaM or its N- and C-terminal subdomains. We found that RUBpep bound to Ca(2+)/CaM with a dissociation constant of 100-300 nm. The C-terminal subdomain of CaM preferentially bound to RUBpep with an affinity 12.5-fold stronger than the N-terminal subdomain. Fluorescence, circular dichroism and NMR spectroscopic studies revealed a "wrapping around" mode of interaction between RUBpep and Ca(2+)/CaM with substantially more helical structure in RUBpep and a global structural change in CaM upon complex formation. Using a site-directed mutagenesis approach, we further demonstrated that association of CaM with the CaM-binding domain in the RUBV NS protease was necessary for NS protease activity and infectivity.
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Affiliation(s)
- Yubin Zhou
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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23
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Maniccia AW, Yang W, Johnson JA, Li S, Tjong H, Zhou HX, Shaket LA, Yang JJ. Inverse tuning of metal binding affinity and protein stability by altering charged coordination residues in designed calcium binding proteins. PMC BIOPHYSICS 2009; 2:11. [PMID: 20025729 PMCID: PMC2816670 DOI: 10.1186/1757-5036-2-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 12/21/2009] [Indexed: 11/10/2022]
Abstract
Ca(2+ )binding proteins are essential for regulating the role of Ca(2+ )in cell signaling and maintaining Ca(2+ )homeostasis. Negatively charged residues such as Asp and Glu are often found in Ca(2+ )binding proteins and are known to influence Ca(2+ )binding affinity and protein stability. In this paper, we report a systematic investigation of the role of local charge number and type of coordination residues in Ca(2+ )binding and protein stability using de novo designed Ca(2+ )binding proteins. The approach of de novo design was chosen to avoid the complications of cooperative binding and Ca(2+)-induced conformational change associated with natural proteins. We show that when the number of negatively charged coordination residues increased from 2 to 5 in a relatively restricted Ca(2+)-binding site, Ca(2+ )binding affinities increased by more than 3 orders of magnitude and metal selectivity for trivalent Ln(3+ )over divalent Ca(2+ )increased by more than 100-fold. Additionally, the thermal transition temperatures of the apo forms of the designed proteins decreased due to charge repulsion at the Ca(2+ )binding pocket. The thermal stability of the proteins was regained upon Ca(2+ )and Ln(3+ )binding to the designed Ca(2+ )binding pocket. We therefore observe a striking tradeoff between Ca(2+)/Ln(3+ )affinity and protein stability when the net charge of the coordination residues is varied. Our study has strong implications for understanding and predicting Ca(2+)-conferred thermal stabilization of natural Ca(2+ )binding proteins as well as for designing novel metalloproteins with tunable Ca(2+ )and Ln(3+ )binding affinity and selectivity.PACS codes: 05.10.-a.
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Affiliation(s)
- Anna Wilkins Maniccia
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Wei Yang
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Renmin Road 5625, Changchun, Jilin 130022, PR China
| | - Julian A Johnson
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Shunyi Li
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Harianto Tjong
- Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Lev A Shaket
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Jenny J Yang
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
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24
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Wang X, Kirberger M, Qiu F, Chen G, Yang JJ. Towards predicting Ca2+-binding sites with different coordination numbers in proteins with atomic resolution. Proteins 2009; 75:787-98. [PMID: 19003991 DOI: 10.1002/prot.22285] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ca(2+)-binding sites in proteins exhibit a wide range of polygonal geometries that directly relate to an equally-diverse set of biological functions. Although the highly-conserved EF-Hand motif has been studied extensively, non-EF-Hand sites exhibit much more structural diversity which has inhibited efforts to determine the precise location of Ca(2+)-binding sites, especially for sites with few coordinating ligands. Previously, we established an algorithm capable of predicting Ca(2+)-binding sites using graph theory to identify oxygen clusters comprised of four atoms lying on a sphere of specified radius, the center of which was the predicted calcium position. Here we describe a new algorithm, MUG (MUltiple Geometries), which predicts Ca(2+)-binding sites in proteins with atomic resolution. After first identifying all the possible oxygen clusters by finding maximal cliques, a calcium center (CC) for each cluster, corresponding to the potential Ca(2+) position, is located to maximally regularize the structure of the (cluster, CC) pair. The structure is then inspected by geometric filters. An unqualified (cluster, CC) pair is further handled by recursively removing oxygen atoms and relocating the CC until its structure is either qualified or contains fewer than four ligand atoms. Ligand coordination is then determined for qualified structures. This algorithm, which predicts both Ca(2+) positions and ligand groups, has been shown to successfully predict over 90% of the documented Ca(2+)-binding sites in three datasets of highly-diversified protein structures with 0.22 to 0.49 A accuracy. All multiple-binding sites (i.e. sites with a single ligand atom associated with multiple calcium ions) were predicted, as were half of the low-coordination sites (i.e. sites with less than four protein ligand atoms) and 14/16 cofactor-coordinating sites. Additionally, this algorithm has the flexibility to incorporate surface water molecules and protein cofactors to further improve the prediction for low-coordination and cofactor-coordinating Ca(2+)-binding sites.
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Affiliation(s)
- Xue Wang
- Department of Computer Science, Georgia State University, Atlanta, Georgia 30303, USA
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25
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Philominathan STL, Matsushita O, Gensure R, Sakon J. Ca2+-induced linker transformation leads to a compact and rigid collagen-binding domain of Clostridium histolyticum collagenase. FEBS J 2009; 276:3589-601. [PMID: 19490118 DOI: 10.1111/j.1742-4658.2009.07078.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Clostridium histolyticum collagenase is responsible for extensive tissue destruction in gas gangrene, and its activity is enhanced by calcium ions. The collagen-binding domain is the minimal segment of the enzyme required for binding to insoluble collagen fibrils and for subsequent collagenolysis. The collagen-binding domain is joined to another binding module by a conserved 14-amino-acid linker. The linker undergoes secondary structural transformation from an alpha-helix to a beta-strand and forms a nonprolyl cis-peptide in the presence of calcium ions. In this study, various biophysical methods were utilized to better understand the structure and functional role of the novel calcium-activated linker. Two Ca(2+) ions bind cooperatively with macroscopic association constants of K(1) = 5.01 x 10(5) m(-1) and K(2) = 2.28 x 10(5) m(-1). The chelation of the second calcium ion is enthalpically unfavorable, which could be a result of isomerization of the nonprolyl cis-peptide. The holo protein is more stable than the apo protein against thermal denaturation (DeltaT(m) approximately 20 degrees C) and chemical denaturation (DeltaDeltaG(H2O) approximately 3 kcal x mol(-1) for urea or guanidine HCl denaturation and Delta20% v/v in 2,2,2-trifluoroethanol). The compact holo collagen-binding domain is more resistant to proteolytic digestion than the apo collagen-binding domain. The orientation of the linker appears to play a crucial role in the stability and dynamics of the collagen-binding domain.
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26
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Li S, Yang W, Maniccia AW, Barrow D, Tjong H, Zhou HX, Yang JJ. Rational design of a conformation-switchable Ca2+- and Tb3+-binding protein without the use of multiple coupled metal-binding sites. FEBS J 2008; 275:5048-61. [PMID: 18785925 DOI: 10.1111/j.1742-4658.2008.06638.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Ca2+, as a messenger of signal transduction, regulates numerous target molecules via Ca2+-induced conformational changes. Investigation into the determinants for Ca2+-induced conformational change is often impeded by cooperativity between multiple metal-binding sites or protein oligomerization in naturally occurring proteins. To dissect the relative contributions of key determinants for Ca2+-dependent conformational changes, we report the design of a single-site Ca2+-binding protein (CD2.trigger) created by altering charged residues at an electrostatically sensitive location on the surface of the host protein rat Cluster of Differentiation 2 (CD2).CD2.trigger binds to Tb3+ and Ca2+ with dissociation constants of 0.3 +/- 0.1 and 90 +/- 25 microM, respectively. This protein is largely unfolded in the absence of metal ions at physiological pH, but Tb3+ or Ca2+ binding results in folding of the native-like conformation. Neutralization of the charged coordination residues, either by mutation or protonation, similarly induces folding of the protein. The control of a major conformational change by a single Ca2+ ion, achieved on a protein designed without reliance on sequence similarity to known Ca2+-dependent proteins and coupled metal-binding sites, represents an important step in the design of trigger proteins.
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Affiliation(s)
- Shunyi Li
- Department of Chemistry, Center of Drug Design and Biotechnology, Georgia State University, Atlanta, GA, USA
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27
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Kirberger M, Yang JJ. Structural differences between Pb2+- and Ca2+-binding sites in proteins: implications with respect to toxicity. J Inorg Biochem 2008; 102:1901-9. [PMID: 18684507 DOI: 10.1016/j.jinorgbio.2008.06.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Revised: 06/20/2008] [Accepted: 06/23/2008] [Indexed: 11/19/2022]
Abstract
Pb(2+) is known to displace physiologically-relevant metal ions in proteins. To investigate potential relationships between Pb(2+)/protein complexes and toxicity, data from the protein data bank were analyzed to compare structural properties of Pb(2+)- and Ca(2+)-binding sites. Results of this analysis reveal that the majority of Pb(2+) sites (77.1%) involve 2-5 binding ligands, compared with 6+/-2 for non-EF-Hand and 7+/-1 for EF-Hand Ca(2+)-binding sites. The mean net negative charge by site (1.7) fell between values noted for non-EF-Hand (1+/-1) and EF-Hand (3+/-1). Oxygen is the dominant ligand for both Pb(2+) and Ca(2+), but Pb(2+) binds predominantly with sidechain Glu (38.4%), which is less prevalent in both non-EF-Hand (10.4%) and EF-Hand (26.6%) Ca(2+)-binding sites. A comparison of binding geometries where Pb(2+) has replaced Ca(2+) in calmodulin (CaM) and Zn(2+) in 5-aminolaevulinic acid dehydratase (ALAD) revealed protein structural changes that appear to be unrelated to ionic displacement. Structural changes observed with CaM may be related to opportunistic binding of Pb(2+) in regions of high electrostatic charge, whereas ALAD may bind multiple Pb(2+) ions in the active site. These results suggest that Pb(2+) adapts to structurally-diverse binding geometries and that opportunistic binding may play an active role in molecular metal toxicity.
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Affiliation(s)
- Michael Kirberger
- Center for Drug Design and Biotechnology, Department of Chemistry, Georgia State University, 50 Decatur Street, 550 NSC, Atlanta, GA 30303, USA
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Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal ions in biological catalysis: from enzyme databases to general principles. J Biol Inorg Chem 2008; 13:1205-18. [PMID: 18604568 DOI: 10.1007/s00775-008-0404-5] [Citation(s) in RCA: 727] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 06/25/2008] [Indexed: 12/01/2022]
Abstract
We analysed the roles and distribution of metal ions in enzymatic catalysis using available public databases and our new resource Metal-MACiE (http://www.ebi.ac.uk/thornton-srv/databases/Metal_MACiE/home.html). In Metal-MACiE, a database of metal-based reaction mechanisms, 116 entries covering 21% of the metal-dependent enzymes and 70% of the types of enzyme-catalysed chemical transformations are annotated according to metal function. We used Metal-MACiE to assess the functions performed by metals in biological catalysis and the relative frequencies of different metals in different roles, which can be related to their individual chemical properties and availability in the environment. The overall picture emerging from the overview of Metal-MACiE is that redox-inert metal ions are used in enzymes to stabilize negative charges and to activate substrates by virtue of their Lewis acid properties, whereas redox-active metal ions can be used both as Lewis acids and as redox centres. Magnesium and zinc are by far the most common ions of the first type, while calcium is relatively less used. Magnesium, however, is most often bound to phosphate groups of substrates and interacts with the enzyme only transiently, whereas the other metals are stably bound to the enzyme. The most common metal of the second type is iron, which is prevalent in the catalysis of redox reactions, followed by manganese, cobalt, molybdenum, copper and nickel. The control of the reactivity of redox-active metal ions may involve their association with organic cofactors to form stable units. This occurs sometimes for iron and nickel, and quite often for cobalt and molybdenum.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
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Statistical analysis of structural characteristics of protein Ca2+-binding sites. J Biol Inorg Chem 2008; 13:1169-81. [PMID: 18594878 DOI: 10.1007/s00775-008-0402-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 06/17/2008] [Indexed: 10/21/2022]
Abstract
To better understand the biological significance of Ca(2+), we report a comprehensive statistical analysis of calcium-binding proteins from the Protein Data Bank to identify structural parameters associated with EF-hand and non-EF-hand Ca(2+)-binding sites. Comparatively, non-EF-hand sites utilize lower coordination numbers (6 +/- 2 vs. 7 +/- 1), fewer protein ligands (4 +/- 2 vs. 6 +/- 1), and more water ligands (2 +/- 2 vs. 1 +/- 0) than EF-hand sites. The orders of ligand preference for non-EF-hand and EF-hand sites, respectively, were H(2)O (33.1%) > side-chain Asp (24.5%) > main-chain carbonyl (23.9%) > side-chain Glu (10.4%), and side-chain Asp (29.7%) > side-chain Glu (26.6%) > main-chain carbonyl (21.4%) > H(2)O (13.3%). Less formal negative charge was observed in the non-EF-hand than in the EF-hand binding sites (1 +/- 1 vs. 3 +/- 1). Additionally, over 20% of non-EF-hand sites had formal charge values of zero due to increased utilization of water and carbonyl oxygen ligands. Moreover, the EF-hand sites presented a narrower range of ligand distances and bond angles than non-EF-hand sites, possibly owing to the highly conserved helix-loop-helix motif. Significant differences between ligand types (carbonyl, side chain, bidentate) demonstrated that angles associated with each type must be classified separately, and the EF-hand side-chain Ca-O-C angles exhibited an unusual bimodal quality consistent with an Asp distribution that differed from the Gaussian model observed for non-EF-hand proteins. The results of this survey more accurately describe differences between EF-hand and non-EF-hand proteins and provide new parameters for the prediction and design of different classes of Ca(2+)-binding proteins.
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Beck MR, DeKoster GT, Hambly DM, Gross ML, Cistola DP, Goldman WE. Structural features responsible for the biological stability of Histoplasma's virulence factor CBP. Biochemistry 2008; 47:4427-38. [PMID: 18361504 DOI: 10.1021/bi701495v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The virulence factor CBP is the most abundant protein secreted by Histoplasma capsulatum, a pathogenic fungus that causes histoplasmosis. Although the biochemical function and pathogenic mechanism of CBP are unknown, quantitative Ca (2+) binding measurements indicate that CBP has a strong affinity for calcium ( K D = 6.45 +/- 0.4 nM). However, no change in structure was observed upon binding of calcium, prompting a more thorough investigation of the molecular properties of CBP with respect to self-association, secondary structure, and stability. Over a wide range of pH values and salt concentrations, CBP exists predominantly as a stable, noncovalent homodimer in both its calcium-free and -bound states. Solution-state NMR and circular dichroism (CD) measurements indicated that the protein is largely alpha-helical, and its secondary structure content changes little over the range of pH values encountered physiologically. ESI-MS revealed that the six cysteine residues of CBP are involved in three intramolecular disulfide bonds that help maintain a highly protease resistant structure. Thermally and chemically induced denaturation studies indicated that unfolding of disulfide-intact CBP is reversible and provided quantitative measurements of protein stability. This disulfide-linked, protease resistant, homodimeric alpha-helical structure of CBP is likely to be advantageous for a virulence factor that must survive the harsh environment within the phagolysosomes of host macrophages.
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Affiliation(s)
- Moriah R Beck
- Department of Molecular Microbiology, Washington University, St. Louis, Missouri 63110, USA
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31
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Mastoparan/Mastoparan X altered binding behavior of La3+ to calmodulin in ternary complexes. J Inorg Biochem 2008; 102:278-84. [DOI: 10.1016/j.jinorgbio.2007.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 07/19/2007] [Accepted: 08/30/2007] [Indexed: 11/21/2022]
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32
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Scheschonka A, Findlow S, Schemm R, El Far O, Caldwell JH, Crump MP, Holden-Dye K, O'Connor V, Betz H, Werner JM. Structural determinants of calmodulin binding to the intracellular C-terminal domain of the metabotropic glutamate receptor 7A. J Biol Chem 2007; 283:5577-88. [PMID: 18089570 DOI: 10.1074/jbc.m709505200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Calmodulin (CaM) binds in a Ca2+-dependent manner to the intracellular C-terminal domains of most group III metabotropic glutamate receptors (mGluRs). Here we combined mutational and biophysical approaches to define the structural basis of CaM binding to mGluR 7A. Ca2+/CaM was found to interact with mGluR 7A primarily via its C-lobe at a 1:1 CaM:C-tail stoichiometry. Pulldown experiments with mutant CaM and mGluR 7A C-tail constructs and high resolution NMR with peptides corresponding to the CaM binding region of mGluR 7A allowed us to define hydrophobic and ionic interactions required for Ca2+/CaM binding and identified a 1-8-14 CaM-binding motif. The Ca2+/CaM.mGluR 7A peptide complex displays a classical wraparound structure that closely resembles that formed by Ca2+/CaM upon binding to smooth muscle myosin light chain kinase. Our data provide insight into how Ca2+/CaM regulates group III mGluR signaling via competition with intracellular proteins for receptor-binding sites.
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Affiliation(s)
- Astrid Scheschonka
- Department of Neurochemistry, Max Planck Institute for Brain Research, 60528 Frankfurt, Germany
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33
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Gifford JL, Walsh MP, Vogel HJ. Structures and metal-ion-binding properties of the Ca2+-binding helix–loop–helix EF-hand motifs. Biochem J 2007; 405:199-221. [PMID: 17590154 DOI: 10.1042/bj20070255] [Citation(s) in RCA: 630] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The ‘EF-hand’ Ca2+-binding motif plays an essential role in eukaryotic cellular signalling, and the proteins containing this motif constitute a large and functionally diverse family. The EF-hand is defined by its helix–loop–helix secondary structure as well as the ligands presented by the loop to bind the Ca2+ ion. The identity of these ligands is semi-conserved in the most common (the ‘canonical’) EF-hand; however, several non-canonical EF-hands exist that bind Ca2+ by a different co-ordination mechanism. EF-hands tend to occur in pairs, which form a discrete domain so that most family members have two, four or six EF-hands. This pairing also enables communication, and many EF-hands display positive co-operativity, thereby minimizing the Ca2+ signal required to reach protein saturation. The conformational effects of Ca2+ binding are varied, function-dependent and, in some cases, minimal, but can lead to the creation of a protein target interaction site or structure formation from a molten-globule apo state. EF-hand proteins exhibit various sensitivities to Ca2+, reflecting the intrinsic binding ability of the EF-hand as well as the degree of co-operativity in Ca2+ binding to paired EF-hands. Two additional factors can influence the ability of an EF-hand to bind Ca2+: selectivity over Mg2+ (a cation with very similar chemical properties to Ca2+ and with a cytoplasmic concentration several orders of magnitude higher) and interaction with a protein target. A structural approach is used in this review to examine the diversity of family members, and a biophysical perspective provides insight into the ability of the EF-hand motif to bind Ca2+ with a wide range of affinities.
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Affiliation(s)
- Jessica L Gifford
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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Chazin WJ. The impact of X-ray crystallography and NMR on intracellular calcium signal transduction by EF-hand proteins: crossing the threshold from structure to biology and medicine. ACTA ACUST UNITED AC 2007; 2007:pe27. [PMID: 17536097 DOI: 10.1126/stke.3882007pe27] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The use of x-ray crystallography and solution nuclear magnetic resonance (NMR) spectroscopy has revolutionized our understanding of the transduction of intracellular calcium signals into cellular responses. Indeed, the ability to cross a critical threshold from basic descriptive structural biochemistry to real-world applications in therapeutics and biotechnology now looms on the experimental horizon. The ~500 atomic resolution structures determined by x-ray and NMR approaches and deposited in the Protein Data Bank, many of which are of complexes of EF-hand proteins with peptide fragments of cellular targets, have yielded an extremely thorough description for how EF-hand proteins respond to the binding of calcium. Although this database of structures is a powerful structural tool to describe EF-hand protein function, it is limited in its ability to have a significant impact on biology and medicine because the structural effects on the downstream target are not determined. The opportunity that now lies before us is to extend this EF-hand-centric structural information so that the alterations in the target proteins are defined and the structural basis for functional consequences downstream is understood.
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Affiliation(s)
- Walter J Chazin
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-8725, USA.
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35
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Zhou Y, Tzeng WP, Yang W, Zhou Y, Ye Y, Lee HW, Frey TK, Yang J. Identification of a Ca2+-binding domain in the rubella virus nonstructural protease. J Virol 2007; 81:7517-28. [PMID: 17475644 PMCID: PMC1933374 DOI: 10.1128/jvi.00605-07] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The rubella virus (RUB) nonstructural protein (NS) open reading frame (ORF) encodes a polypeptide precursor that is proteolytically self cleaved into two replicase components involved in viral RNA replication. A putative EF-hand Ca(2+)-binding motif that was conserved across different genotypes of RUB was predicted within the nonstructural protease that cleaves the precursor by using bioinformatics tools. To probe the metal-binding properties of this motif, we used an established grafting approach and engineered the 12-residue Ca(2+)-coordinating loop into a non-Ca(2+)-binding scaffold protein, CD2. The grafted EF-loop bound to Ca(2+) and its trivalent analogs Tb(3+) and La(3+) with K(d)s of 214, 47, and 14 microM, respectively. Mutations (D1210A and D1217A) of two of the potential Ca(2+)-coordinating ligands in the EF-loop led to the elimination of Tb(3+) binding. Inductive coupled plasma mass spectrometry was used to confirm the presence of Ca(2+) ([Ca(2+)]/[protein] = 0.7 +/- 0.2) in an NS protease minimal metal-binding domain, RUBCa, that spans the EF-hand motif. Conformational studies on RUBCa revealed that Ca(2+) binding induced local conformational changes and increased thermal stability (Delta T(m) = 4.1 degrees C). The infectivity of an RUB infectious cDNA clone containing the mutations D1210A/D1217A was decreased by approximately 20-fold in comparison to the wild-type (wt) clone, and these mutations rapidly reverted to the wt sequence. The NS protease containing these mutations was less efficient at precursor cleavage than the wt NS protease at 35 degrees C, and the mutant NS protease was temperature sensitive at 39 degrees C, confirming that the Ca(2+)-binding loop played a structural role in the NS protease and was specifically required for optimal stability under physiological conditions.
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Affiliation(s)
- Yubin Zhou
- Department of Chemistry, Georgia State University, 50 Decatur St., Atlanta, GA 30303, USA
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36
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Lakowski TM, Lee GM, Okon M, Reid RE, McIntosh LP. Calcium-induced folding of a fragment of calmodulin composed of EF-hands 2 and 3. Protein Sci 2007; 16:1119-32. [PMID: 17473011 PMCID: PMC2206659 DOI: 10.1110/ps.072777107] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Calmodulin (CaM) is an EF-hand protein composed of two calcium (Ca(2+))-binding EF-hand motifs in its N-domain (EF-1 and EF-2) and two in its C-domain (EF-3 and EF-4). In this study, we examined the structure, dynamics, and Ca(2+)-binding properties of a fragment of CaM containing only EF-2 and EF-3 and the intervening linker sequence (CaM2/3). Based on NMR spectroscopic analyses, Ca(2+)-free CaM2/3 is predominantly unfolded, but upon binding Ca(2+), adopts a monomeric structure composed of two EF-hand motifs bridged by a short antiparallel beta-sheet. Despite having an "even-odd" pairing of EF-hands, the tertiary structure of CaM2/3 is similar to both the "odd-even" paired N- and C-domains of Ca(2+)-ligated CaM, with the conformationally flexible linker sequence adopting the role of an inter-EF-hand loop. However, unlike either CaM domain, CaM2/3 exhibits stepwise Ca(2+) binding with a K (d1) = 30 +/- 5 microM to EF-3, and a K (d2) > 1000 microM to EF-2. Binding of the first equivalent of Ca(2+) induces the cooperative folding of CaM2/3. In the case of native CaM, stacking interactions between four conserved aromatic residues help to hold the first and fourth helices of each EF-hand domain together, while the loop between EF-hands covalently tethers the second and third helices. In contrast, these aromatic residues lie along the second and third helices of CaM2/3, and thus are positioned adjacent to the loop between its "even-odd" paired EF-hands. This nonnative hydrophobic core packing may contribute to the weak Ca(2+) affinity exhibited by EF-2 in the context of CaM2/3.
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Affiliation(s)
- Ted M Lakowski
- Faculty of Pharmaceutical Sciences, Division of Biomolecular and Pharmaceutical Chemistry, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
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37
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Doerner JF, Gisselmann G, Hatt H, Wetzel CH. Transient receptor potential channel A1 is directly gated by calcium ions. J Biol Chem 2007; 282:13180-9. [PMID: 17353192 DOI: 10.1074/jbc.m607849200] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the superfamily of transient receptor potential (TRP) channels are proposed to play important roles in sensory physiology. As an excitatory ion channel TRPA1 is robustly activated by pungent irritants in mustard and garlic and is suggested to mediate the inflammatory actions of environmental irritants and proalgesic agents. Here, we demonstrate that, in addition to pungent natural compounds, Ca(2+) directly gates heterologously expressed TRPA1 in whole-cell and excised-patch recordings with an apparent EC(50) of 905 nm. Pharmacological experiments and site-directed mutagenesis indicate that the N-terminal EF-hand calcium-binding domain of the channel is involved in Ca(2+)-dependent activation. Furthermore, we determine Ca(2+) as prerequisite for icilin activity on TRPA1.
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Affiliation(s)
- Julia F Doerner
- Lehrstuhl fuer Zellphysiologie, Fakultaet Biologie, Ruhr-Universitaet Bochum, 44780 Bochum, Germany
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38
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Structural aspects of calcium-binding proteins and their interactions with targets. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/s0167-7306(06)41004-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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39
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Stathopulos PB, Li GY, Plevin MJ, Ames JB, Ikura M. Stored Ca2+ depletion-induced oligomerization of stromal interaction molecule 1 (STIM1) via the EF-SAM region: An initiation mechanism for capacitive Ca2+ entry. J Biol Chem 2006; 281:35855-62. [PMID: 17020874 DOI: 10.1074/jbc.m608247200] [Citation(s) in RCA: 321] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Stromal interaction molecule 1 (STIM1) has recently been identified as a key player in store-operated Ca2+ entry. Endoplasmic reticulum (ER) luminal Ca2+ depletion results in STIM1 redistribution from ER membrane homogeneity to distinctly localized aggregates near the plasma membrane; these changes precede and are linked to cytoplasmic Ca2+ influx via Ca2+ release-activated channels (CRACs). The molecular mechanisms initiating ER STIM1 redistribution and plasma membrane CRAC activity are not well understood. We recombinantly expressed the Ca2+-sensing region of STIM1 consisting of the EF-hand together with the sterile alpha-motif (SAM) domain (EF-SAM) to investigate its Ca2+-related conformational and biochemical features. We demonstrate that Ca2+-loaded EF-SAM (holo) contains high alpha-helicity, whereas EF-SAM in the absence of Ca2+ (apo) is much less compact. Accordingly, the melting temperature (Tm) of the holoform is approximately 25 degrees C higher than apoform; heat and urea-derived thermodynamic parameters indicate a Ca2+-induced stabilization of 3.2 kcal mol(-1). We show that holoEF-SAM exists as a monomer, whereas apoEF-SAM readily forms a dimer and/or oligomer, and that oligomer to monomer transitions and vice versa are at least in part mediated by changes in surface hydrophobicity. Additionally, we find that the Ca2+ binding affinity of EF-SAM is relatively low with an apparent dissociation constant (Kd) of approximately 0.2-0.6 mM and a binding stoichiometry of 1. Our results suggest that EF-SAM actively participates in and is the likely the molecular trigger initiating STIM1 punctae formation via large conformational changes. The low Ca2+ affinity of EF-SAM is reconciled with the confirmed role of STIM1 as an ER Ca2+ sensor.
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Affiliation(s)
- Peter B Stathopulos
- Division of Signaling Biology and Department of Medical Biophysics, Ontario Cancer Institute and University of Toronto, Toronto M5G 1L7, Ontario, Canada
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40
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Deng H, Chen G, Yang W, Yang JJ. Predicting calcium-binding sites in proteins - a graph theory and geometry approach. Proteins 2006; 64:34-42. [PMID: 16617426 DOI: 10.1002/prot.20973] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Identifying calcium-binding sites in proteins is one of the first steps towards predicting and understanding the role of calcium in biological systems for protein structure and function studies. Due to the complexity and irregularity of calcium-binding sites, a fast and accurate method for predicting and identifying calcium-binding protein is needed. Here we report our development of a new fast algorithm (GG) to detect calcium-binding sites. The GG algorithm uses a graph theory algorithm to find oxygen clusters of the protein and a geometric algorithm to identify the center of these clusters. A cluster of four or more oxygen atoms has a high potential for calcium binding. High performance with about 90% site sensitivity and 80% site selectivity has been obtained for three datasets containing a total of 123 proteins. The results suggest that a sphere of a certain size with four or more oxygen atoms on the surface and without other atoms inside is necessary and sufficient for quickly identifying the majority of the calcium-binding sites with high accuracy. Our finding opens a new avenue to visualize and analyze calcium-binding sites in proteins facilitating the prediction of functions from structural genomic information.
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Affiliation(s)
- Hai Deng
- Department of Computer Science, Georgia State University, Atlanta, Georgia 30302, USA
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41
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Green JL, Martin SR, Fielden J, Ksagoni A, Grainger M, Yim Lim BYS, Molloy JE, Holder AA. The MTIP-myosin A complex in blood stage malaria parasites. J Mol Biol 2005; 355:933-41. [PMID: 16337961 DOI: 10.1016/j.jmb.2005.11.027] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Revised: 11/04/2005] [Accepted: 11/09/2005] [Indexed: 10/25/2022]
Abstract
Parasites of the Apicomplexa phylum use an actomyosin motor to drive invasion of host cells. The motor complex is located at the parasite's periphery between the plasma membrane and an inner membrane complex. A crucial component of this complex is myosin tail domain interacting protein (MTIP) identified in the murine malaria parasite Plasmodium yoelii. Here, we show that MTIP is expressed in Plasmodium falciparum merozoites, localises to the periphery of the cell and is present in a complex with myosin A. The MTIP-myosin A tail interaction has a Kd of 235 nM and calcium ions do not play a role in modulating the binding affinity of the two molecules, despite reports of a predicted EF-hand in MTIP. Antibodies to MTIP were used to immobilise the MTIP-myosin A complex, allowing actin binding and motility to be examined. Measurement of actin filament velocities powered by myosin A revealed a velocity of 3.51 microm s(-1), a speed comparable to fast muscle myosins. A short peptide derived from the tail of myosin A (C-MyoA) bound to MTIP and was able to disrupt the association of MTIP and myosin A in parasite lysates. C-MyoA peptidomimetic compounds that disrupt the MTIP-myosin A interaction are predicted to inhibit parasite motility and host cell invasion, which may be targets for new therapeutic approaches.
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Affiliation(s)
- Judith L Green
- Division of Parasitology, MRC National Institute for Medical Research, London NW7 1AA, UK.
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42
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Patel SP, Campbell DL. Transient outward potassium current, 'Ito', phenotypes in the mammalian left ventricle: underlying molecular, cellular and biophysical mechanisms. J Physiol 2005; 569:7-39. [PMID: 15831535 PMCID: PMC1464208 DOI: 10.1113/jphysiol.2005.086223] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/07/2005] [Accepted: 04/13/2005] [Indexed: 11/08/2022] Open
Abstract
At least two functionally distinct transient outward K(+) current (I(to)) phenotypes can exist across the free wall of the left ventricle (LV). Based upon their voltage-dependent kinetics of recovery from inactivation, these two phenotypes are designated 'I(to,fast)' (recovery time constants on the order of tens of milliseconds) and 'I(to,slow)' (recovery time constants on the order of thousands of milliseconds). Depending upon species, either I(to,fast), I(to,slow) or both current phenotypes may be expressed in the LV free wall. The expression gradients of these two I(to) phenotypes across the LV free wall are typically heterogeneous and, depending upon species, may consist of functional phenotypic gradients of both I(to,fast) and I(to,slow) and/or density gradients of either phenotype. We review the present evidence (molecular, biophysical, electrophysiological and pharmacological) for Kv4.2/4.3 alpha subunits underlying LV I(to,fast) and Kv1.4 alpha subunits underlying LV I(to,slow) and speculate upon the potential roles of each of these currents in determining frequency-dependent action potential characteristics of LV subepicardial versus subendocardial myocytes in different species. We also review the possible functional implications of (i) ancillary subunits that regulate Kv1.4 and Kv4.2/4.3 (Kvbeta subunits, DPPs), (ii) KChIP2 isoforms, (iii) spider toxin-mediated block of Kv4.2/4.3 (Heteropoda toxins, phrixotoxins), and (iv) potential mechanisms of modulation of I(to,fast) and I(to,slow) by cellular redox state, [Ca(2)(+)](i) and kinase-mediated phosphorylation. I(to) phenotypic activation and state-dependent gating models and molecular structure-function relationships are also discussed.
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Affiliation(s)
- Sangita P Patel
- Department of Physiology and Biophysics, University at Buffalo, State University of New York, NY 14214-3078, USA.
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43
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Sheng JZ, Weljie A, Sy L, Ling S, Vogel HJ, Braun AP. Homology modeling identifies C-terminal residues that contribute to the Ca2+ sensitivity of a BKCa channel. Biophys J 2005; 89:3079-92. [PMID: 16100257 PMCID: PMC1366805 DOI: 10.1529/biophysj.105.063610] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Activation of BK(Ca) channels by direct Ca(2+) binding and membrane depolarization occur via independent and additive molecular processes. The "calcium bowl" domain is critically involved in Ca(2+)-dependent gating, and we have hypothesized that a sequence within this domain may resemble an EF hand motif. Using a homology modeling strategy, it was observed that a single Ca(2+) ion may be coordinated by the oxygen-containing side chains of residues within the calcium bowl (i.e., (912)ELVNDTNVQFLD(923)). To examine these predictions directly, alanine-substituted BK(Ca) channel mutants were expressed in HEK 293 cells and the voltage and Ca(2+) dependence of macroscopic currents were examined in inside-out membrane patches. Over the range of 1-10 microM free Ca(2+), single point mutations (i.e., E912A and D923A) produced rightward shifts in the steady-state conductance-voltage relations, whereas the mutants N918A or Q920A had no effect on Ca(2+)-dependent gating. The double mutant E912A/D923A displayed a synergistic shift in Ca(2+)-sensitive gating, as well as altered kinetics of current activation/deactivation. In the presence of 1, 10, and 80 mM cytosolic Mg(2+), this double mutation significantly reduced the Ca(2+)-induced free energy change associated with channel activation. Finally, mutations that altered sensitivity of the holo-channel to Ca(2+) also reduced direct (45)Ca binding to the calcium bowl domain expressed as a bacterial fusion protein. These findings, along with other recent data, are considered in the context of the calcium bowl's high affinity Ca(2+) sensor and the known properties of EF hands.
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Affiliation(s)
- Jian-Zhong Sheng
- Department of Pharmacology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada
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44
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Schymkowitz JWH, Rousseau F, Martins IC, Ferkinghoff-Borg J, Stricher F, Serrano L. Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci U S A 2005; 102:10147-52. [PMID: 16006526 PMCID: PMC1177371 DOI: 10.1073/pnas.0501980102] [Citation(s) in RCA: 280] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The empirical force field Fold-X was developed previously to allow rapid free energy calculations in proteins. Here, we present an enhanced version of the force field allowing prediction of the position of structural water molecules and metal ions, together called single atom ligands. Fold-X picks up 76% of water molecules found to interact with two or more polar atoms of proteins in high-resolution crystal structures and predicts their position to within 0.8 A on average. The prediction of metal ion-binding sites have success rates between 90% and 97% depending on the metal, with an overall standard deviation on the position of binding of 0.3-0.6 A. The following metals were included in the force field: Mg2+, Ca2+, Zn2+, Mn2+, and Cu2+. As a result, the current version of Fold-X can accurately decorate a protein structure with biologically important ions and water molecules. Additionally, the free energy of binding of Ca2+ and Zn2+ (i.e., the natural logarithm of the dissociation constant) and its dependence on ionic strength correlate reasonably well with the experimental data available in the literature, allowing one to discriminate between high- and low-affinity binding sites. Importantly, the accuracy of the energy prediction presented here is sufficient to efficiently discriminate between Mg2+, Ca2+, and Zn2+ binding.
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Affiliation(s)
- Joost W H Schymkowitz
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg D-69117, Germany
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45
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Bhattacharya S, Bunick CG, Chazin WJ. Target selectivity in EF-hand calcium binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2004; 1742:69-79. [PMID: 15590057 DOI: 10.1016/j.bbamcr.2004.09.002] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Revised: 08/30/2004] [Accepted: 09/01/2004] [Indexed: 10/26/2022]
Abstract
EF-hand calcium binding proteins have remarkable sequence homology and structural similarity, yet their response to binding of calcium is diverse and they function in a wide range of biological processes. Knowledge of the fine-tuning of EF-hand protein sequences to optimize specific biochemical properties has been significantly advanced over the past 10 years by determination of atomic resolution structures. These data lay the foundation for addressing how functional selectivity is generated from a generic ionic signal. This review presents current ideas about the structural mechanisms that provide the selectivity of different EF-hand proteins for specific cellular targets, using S100 and calmodulin family proteins to demonstrate the critical concepts. Three factors contribute significantly to target selectivity: molecular architecture, response to binding of Ca(2+) ions, and the characteristics of target binding surfaces. Comparisons of calmodulin and S100 proteins provide insights into the role these factors play in facilitating the variety of binding configurations necessary for recognizing a diverse set of targets.
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Affiliation(s)
- Shibani Bhattacharya
- Department of Biochemistry, Center for Structural Biology, 5140 BIOSCI/MRBIII, Vanderbilt University, Nashville, TN 37232-8725, USA
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Tikunova SB, Davis JP. Designing calcium-sensitizing mutations in the regulatory domain of cardiac troponin C. J Biol Chem 2004; 279:35341-52. [PMID: 15205455 DOI: 10.1074/jbc.m405413200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cardiac troponin C belongs to the EF-hand superfamily of calcium-binding proteins and plays an essential role in the regulation of muscle contraction and relaxation. To follow calcium binding and exchange with the regulatory N-terminal domain (N-domain) of human cardiac troponin C, we substituted Phe at position 27 with Trp, making a fluorescent cardiac troponin C(F27W). Trp(27) accurately reported the kinetics of calcium association and dissociation of the N-domain of cardiac troponin C(F27W). To sensitize the N-domain of cardiac troponin C(F27W) to calcium, we individually substituted the hydrophobic residues Phe(20), Val(44), Met(45), Leu(48), and Met(81) with polar Gln. These mutations were designed to increase the calcium affinity of the N-domain of cardiac troponin C by facilitating the movement of helices B and C (BC unit) away from helices N, A, and D (NAD unit). As anticipated, these selected hydrophobic residue substitutions increased the calcium affinity of the regulatory domain of cardiac troponin C(F27W) approximately 2.1-15.2-fold. Surprisingly, the increased calcium affinity caused by the hydrophobic residue substitutions was largely due to faster calcium association rates (2.6-8.7-fold faster) rather than to slower calcium dissociation rates (1.2-2.9-fold slower). The regulatory N-domains of cardiac troponin C(F27W) and its mutants were also able to bind magnesium competitively and with physiologically relevant affinities (1.2-2.7 mm). The design of calcium-sensitizing cardiac troponin C mutants presented in this work enhances the understanding of how to control cation binding properties of EF-hand proteins and ultimately their structure and physiological function.
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Affiliation(s)
- Svetlana B Tikunova
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio 43210, USA.
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Likić VA, Strehler EE, Gooley PR. Dynamics of Ca2+-saturated calmodulin D129N mutant studied by multiple molecular dynamics simulations. Protein Sci 2004; 12:2215-29. [PMID: 14500879 PMCID: PMC2366934 DOI: 10.1110/ps.0377803] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Fifteen independent 1-nsec MD simulations of fully solvated Ca(2+) saturated calmodulin (CaM) mutant D129N were performed from different initial conditions to provide a sufficient statistical basis to gauge the significance of observed dynamical properties. In all MD simulations the four Ca(2+) ions remained in their binding sites, and retained a single water ligand as observed in the crystal structure. The coordination of Ca(2+) ions in EF-hands I, II, and III was sevenfold. In EF-hand IV, which was perturbed by the mutation of a highly conserved Asp129, an anomalous eightfold Ca(2+) coordination was observed. The Ca(2+) binding loop in EF-hand II was observed to dynamically sample conformations related to the Ca(2+)-free form. Repeated MD simulations implicate two well-defined conformations of Ca(2+) binding loop II, whereas similar effect was not observed for loops I, III, and IV. In 8 out of 15 MD simulations Ca(2+) binding loop II adopted an alternative conformation in which the Thr62 >C=O group was displaced from the Ca(2+) coordination by a water molecule, resulting in the Ca(2+) ion ligated by two water molecules. The alternative conformation of the Ca(2+) binding loop II appears related to the "closed" state involved in conformational exchange previously detected by NMR in the N-terminal domain fragment of CaM and the C-terminal domain fragment of the mutant E140Q. MD simulations suggest that conformations involved in microsecond exchange exist partially preformed on the nanosecond time scale.
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Affiliation(s)
- Vladimir A Likić
- Department of Biochemistry and Molecular Biology, Russell Grimwade School of Biochemistry, The University of Melbourne, Parkville, VIC 3052, Australia.
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Wingo TL, Shah VN, Anderson ME, Lybrand TP, Chazin WJ, Balser JR. An EF-hand in the sodium channel couples intracellular calcium to cardiac excitability. Nat Struct Mol Biol 2004; 11:219-25. [PMID: 14981509 DOI: 10.1038/nsmb737] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2003] [Accepted: 01/29/2004] [Indexed: 11/09/2022]
Abstract
Sodium channels initiate the electrical cascade responsible for cardiac rhythm, and certain life-threatening arrhythmias arise from Na(+) channel dysfunction. We propose a novel mechanism for modulation of Na(+) channel function whereby calcium ions bind directly to the human cardiac Na(+) channel (hH1) via an EF-hand motif in the C-terminal domain. A functional role for Ca(2+) binding was identified electrophysiologically, by measuring Ca(2+)-induced modulation of hH1. A small hH1 fragment containing the EF-hand motif was shown to form a structured domain and to bind Ca(2+) with affinity characteristic of calcium sensor proteins. Mutations in this domain reduce Ca(2+) affinity in vitro and the inactivation gating effects of Ca(2+) in electrophysiology experiments. These studies reveal the molecular basis for certain forms of long QT syndrome and other arrhythmia-producing syndromes, and suggest a potential pharmacological target for antiarrhythmic drug design.
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Affiliation(s)
- Tammy L Wingo
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, USA
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Wakabayashi H, Freas J, Zhou Q, Fay PJ. Residues 110-126 in the A1 domain of factor VIII contain a Ca2+ binding site required for cofactor activity. J Biol Chem 2004; 279:12677-84. [PMID: 14722121 DOI: 10.1074/jbc.m311042200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Generation of factor VIII cofactor activity requires divalent metal ions such as Ca2+ or Mn2+. Evaluation of cofactor reconstitution from isolated factor VIIIa subunits revealed the presence of a functional Ca2+ binding site within the A1 subunit. Isothermal titration calorimetry demonstrated at least two Ca2+ binding sites of similar affinity (K(d) = 0.74 microm) within the A1 subunit. Mutagenesis of an acidic residue-rich region in the A1 domain (residues 110-126) homologous to a putative Ca2+ binding site in factor V (Zeibdawi, A. R., and Pryzdial, E. L. (2001) J. Biol. Chem. 276, 19929-19936) and expression of B-domainless factor VIII molecules yielded reagents to probe Ca2+ and Mn2+ binding in a functional assay. Basal activity observed for wild type factor VIII in a metal ion-free buffer was enhanced approximately 2-fold with saturating Ca2+ or Mn2+ and yielded functional K(d) values of 1.2 and 1.40 microm, respectively. Ca2+ binding affinity was greatly reduced (or lost) in several mutants including E110A, E110D, D116A, E122A, D125A, and D126A. Alternatively, E113A, D115A, and E124A showed wild type-like activity with little or no reduction in Ca2+ affinity. However, Mn2+ affinity was minimally altered except for mutant D125A (and D116A). These results are consistent with region 110-126 serving a critical role for Ca2+ coordination with selected residues capable of contributing to a partially overlapping site for Mn2+, and that occupancy of either site is required for maximal cofactor activity.
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Affiliation(s)
- Hironao Wakabayashi
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, 601 Elmwood Avenue, Rochester, NY 14642, USA
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Abou-Hachem M, Olsson F, Nordberg Karlsson E. Probing the stability of the modular family 10 xylanase from Rhodothermus marinus. Extremophiles 2003; 7:483-91. [PMID: 12942350 DOI: 10.1007/s00792-003-0348-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2003] [Accepted: 07/07/2003] [Indexed: 11/27/2022]
Abstract
The thermophilic bacterium Rhodothermus marinus produces a modular xylanase (Xyn10A) consisting of two N-terminal carbohydrate-binding modules (CBMs), followed by a domain of unknown function, and a catalytic module flanked by a fifth domain. Both Xyn10A CBMs bind calcium ions, and this study explores the effect of these ions on the stability of the full-length enzyme. Xyn10A and truncated forms thereof were produced and their thermostabilities were evaluated under different calcium loads. Studies performed using differential scanning calorimetry showed that the unfolding temperature of the Xyn10A was significantly dependent on the presence of Ca2+, and that the third domain of the enzyme binds at least one Ca2+. Thermal inactivation studies confirmed the role of tightly bound Ca2+ in stabilizing the enzyme, but showed that the presence of a large excess of this ion results in reduced kinetic stability. The truncated forms of Xyn10A were less stable than the full-length enzyme, indicative of module/domain thermostabilizing interactions. Finally, possible roles of the two domains of unknown function are discussed in the light of this study. This is the first report on the thermostabilizing role of calcium on a modular family 10 xylanase that displays multiple calcium binding in three of its five domains/modules.
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Affiliation(s)
- Maher Abou-Hachem
- Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
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