1
|
Abstract
Ca2+ binding proteins (CBP) are of key importance for calcium to play its role as a pivotal second messenger. CBP bind Ca2+ in specific domains, contributing to the regulation of its concentration at the cytosol and intracellular stores. They also participate in numerous cellular functions by acting as Ca2+ transporters across cell membranes or as Ca2+-modulated sensors, i.e. decoding Ca2+ signals. Since CBP are integral to normal physiological processes, possible roles for them in a variety of diseases has attracted growing interest in recent years. In addition, research on CBP has been reinforced with advances in the structural characterization of new CBP family members. In this chapter we have updated a previous review on CBP, covering in more depth potential participation in physiopathological processes and candidacy for pharmacological targets in many diseases. We review intracellular CBP that contain the structural EF-hand domain: parvalbumin, calmodulin, S100 proteins, calcineurin and neuronal Ca2+ sensor proteins (NCS). We also address intracellular CBP lacking the EF-hand domain: annexins, CBP within intracellular Ca2+ stores (paying special attention to calreticulin and calsequestrin), proteins that contain a C2 domain (such as protein kinase C (PKC) or synaptotagmin) and other proteins of interest, such as regucalcin or proprotein convertase subtisilin kexins (PCSK). Finally, we summarise the latest findings on extracellular CBP, classified according to their Ca2+ binding structures: (i) EF-hand domains; (ii) EGF-like domains; (iii) ɣ-carboxyl glutamic acid (GLA)-rich domains; (iv) cadherin domains; (v) Ca2+-dependent (C)-type lectin-like domains; (vi) Ca2+-binding pockets of family C G-protein-coupled receptors.
Collapse
|
2
|
Sun B, Vaughan D, Tikunova S, Creamer TP, Davis JP, Kekenes-Huskey PM. Calmodulin-Calcineurin Interaction beyond the Calmodulin-Binding Region Contributes to Calcineurin Activation. Biochemistry 2019; 58:4070-4085. [PMID: 31483613 DOI: 10.1021/acs.biochem.9b00626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Calcineurin (CaN) is a calcium-dependent phosphatase involved in numerous signaling pathways. Its activation is in part driven by the binding of calmodulin (CaM) to a CaM recognition region (CaMBR) within CaN's regulatory domain (RD). However, secondary interactions between CaM and the CaN RD may be necessary to fully activate CaN. Specifically, it is established that the CaN RD folds upon CaM binding and a region C-terminal to CaMBR, the "distal helix", assumes an α-helix fold and contributes to activation [Dunlap, T. B., et al. (2013) Biochemistry 52, 8643-8651]. We hypothesized in that previous study that this distal helix can bind CaM in a region distinct from the canonical CaMBR. To test this hypothesis, we utilized molecular simulations, including replica-exchange molecular dynamics, protein-protein docking, and computational mutagenesis, to determine potential distal helix-binding sites on CaM's surface. We isolated a potential binding site on CaM (site D) that facilitates moderate-affinity interprotein interactions and predicted that mutation of site D residues K30 and G40 on CaM would weaken CaN distal helix binding. We experimentally confirmed that two variants (K30E and G40D) indicate weaker binding of a phosphate substrate p-nitrophenyl phosphate to the CaN catalytic site by a phosphatase assay. This weakened substrate affinity is consistent with competitive binding of the CaN autoinhibition domain to the catalytic site, which we suggest is due to the weakened distal helix-CaM interactions. This study therefore suggests a novel mechanism for CaM regulation of CaN that may extend to other CaM targets.
Collapse
Affiliation(s)
- Bin Sun
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Darin Vaughan
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Svetlana Tikunova
- Department of Physiology and Cell Biology , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Trevor P Creamer
- Center for Structural Biology and Department of Molecular & Cellular Biochemistry , University of Kentucky , Lexington , Kentucky 40536 , United States
| | - Jonathan P Davis
- Department of Physiology and Cell Biology , The Ohio State University , Columbus , Ohio 43210 , United States
| | - P M Kekenes-Huskey
- Department of Chemical and Materials Engineering , University of Kentucky , Lexington , Kentucky 40506 , United States.,Department of Cell and Molecular Physiology , Loyola University Chicago , Maywood , Illinois 60153 , United States
| |
Collapse
|
3
|
Song R, Li J, Zhang J, Wang L, Tong L, Wang P, Yang H, Wei Q, Cai H, Luo J. Peptides derived from transcription factor EB bind to calcineurin at a similar region as the NFAT-type motif. Biochimie 2017; 142:158-167. [PMID: 28890387 DOI: 10.1016/j.biochi.2017.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/04/2017] [Indexed: 12/16/2022]
Abstract
Calcineurin (CN) is involved in many physiological processes and interacts with multiple substrates. Most of the substrates contain similar motifs recognized by CN. Recent studies revealed a new CN substrate, transcription factor EB (TFEB), which is involved in autophagy. We showed that a 15-mer QSYLENPTSYHLQQS peptide from TFEB (TFEB-YLENP) bound to CN. When the TFEB-YLENP peptide was changed to YLAVP, its affinity for CN increased and it had stronger CN inhibitory activity. Molecular dynamics simulations revealed that the TFEB-YLENP peptide has the same docking sites in CN as the 15-mer DQYLAVPQHPYQWAK motif of the nuclear factor of activated T cells, cytoplasmic 1 (NFATc1-YLAVP). Moreover expression of the NFATc1-YLAVP peptide suppressed the TFEB activation in starved Hela cells. Our studies first identified a CN binding site in TFEB and compared the inhibitory capability of various peptides derived from CN substrates. The data uncovered a diversity in recognition sequences that underlies the CN signaling within the cell. Studies of CN-substrate interactions should lay the groundwork for developing selective CN peptide inhibitors that target CN-substrate interaction in vitro experiments.
Collapse
Affiliation(s)
- Ruiwen Song
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jing Li
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jin Zhang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lu Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Li Tong
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Ping Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Huan Yang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Qun Wei
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Huaibin Cai
- Transgenics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jing Luo
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| |
Collapse
|
4
|
Gyawali R, Zhao Y, Lin J, Fan Y, Xu X, Upadhyay S, Lin X. Pheromone independent unisexual development in Cryptococcus neoformans. PLoS Genet 2017; 13:e1006772. [PMID: 28467481 PMCID: PMC5435349 DOI: 10.1371/journal.pgen.1006772] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/17/2017] [Accepted: 04/20/2017] [Indexed: 11/24/2022] Open
Abstract
The fungus Cryptococcus neoformans can undergo a-α bisexual and unisexual reproduction. Completion of both sexual reproduction modes requires similar cellular differentiation processes and meiosis. Although bisexual reproduction generates equal number of a and α progeny and is far more efficient than unisexual reproduction under mating-inducing laboratory conditions, the α mating type dominates in nature. Population genetic studies suggest that unisexual reproduction by α isolates might have contributed to this sharply skewed distribution of the mating types. However, the predominance of the α mating type and the seemingly inefficient unisexual reproduction observed under laboratory conditions present a conundrum. Here, we discovered a previously unrecognized condition that promotes unisexual reproduction while suppressing bisexual reproduction. Pheromone is the principal stimulus for bisexual development in Cryptococcus. Interestingly, pheromone and other components of the pheromone pathway, including the key transcription factor Mat2, are not necessary but rather inhibitory for Cryptococcus to complete its unisexual cycle under this condition. The inactivation of the pheromone pathway promotes unisexual reproduction despite the essential role of this pathway in non-self-recognition during bisexual reproduction. Nonetheless, the requirement for the known filamentation regulator Znf2 and the expression of hyphal or basidium specific proteins remain the same for pheromone-dependent or independent sexual reproduction. Transcriptome analyses and an insertional mutagenesis screen in mat2Δ identified calcineurin being essential for this process. We further found that Znf2 and calcineurin work cooperatively in controlling unisexual development in this fungus. These findings indicate that Mat2 acts as a repressor of pheromone-independent unisexual development while serving as an activator for a-α bisexual development. The bi-functionality of Mat2 might have allowed it to act as a toggle switch for the mode of sexual development in this ubiquitous eukaryotic microbe.
Collapse
Affiliation(s)
- Rachana Gyawali
- Department of Biology, Texas A&M University, College Station, United States of America
| | - Youbao Zhao
- Department of Biology, Texas A&M University, College Station, United States of America
| | - Jianfeng Lin
- Department of Biology, Texas A&M University, College Station, United States of America
| | - Yumeng Fan
- Department of Biology, Texas A&M University, College Station, United States of America
| | - Xinping Xu
- Department of Biology, Texas A&M University, College Station, United States of America
| | - Srijana Upadhyay
- Department of Biology, Texas A&M University, College Station, United States of America
| | - Xiaorong Lin
- Department of Biology, Texas A&M University, College Station, United States of America
| |
Collapse
|
5
|
Yamamoto T, Sakai H, Sakane F. EF-hand motifs of diacylglycerol kinase α interact intra-molecularly with its C1 domains. FEBS Open Bio 2014; 4:387-92. [PMID: 24918053 PMCID: PMC4050180 DOI: 10.1016/j.fob.2014.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/14/2014] [Accepted: 04/15/2014] [Indexed: 02/02/2023] Open
Abstract
We revealed the intra-molecular interaction of DGKα. The EF-hand motifs of DGKα directly binds to its C1 domains. The intra-molecular interaction was negatively regulated by Ca2+. The intra-molecular interaction is important for the activation mechanism of DGKα.
Diacylglycerol kinase (DGK) α, which is activated by Ca2+, contains a recoverin homology (RVH) domain, tandem repeats of two Ca2+-binding EF-hand motifs, two cysteine-rich C1 domains and the catalytic domain. We previously found that a DGKα mutant lacking the RVH domain and EF-hands was constitutively active and that the N-terminal region of DGKα, consisting of the RVH domain and EF-hand motifs, interacted intra-molecularly with the C-terminal region containing the C1 and catalytic domains. In this study, we narrowed down the interaction regions of DGKα. At the C-terminal region, the C1 domains are responsible for the intra-molecular interaction. At the N-terminal region, the EF-hand motifs mainly contribute to the interaction. Moreover, using highly purified EF-hand motifs and C1 domains, we demonstrate that they directly bind to each other. The co-precipitation of these two domains was clearly attenuated by the addition of Ca2+. These results indicate that the Ca2+-induced dissociation of the intra-molecular interaction between the EF-hand motifs and the C1 domains of DGKα is the key event that regulates the activity of the enzyme.
Collapse
Key Words
- C1 domain
- C1Ds, C1 domains
- CR, catalytic region
- Calcium
- DG, diacylglycerol
- DGK, diacylglycerol kinase
- Diacylglycerol kinase
- EF-hand
- EFHs, EF-hand motifs
- EGFP, enhanced green fluorescence protein
- EGTA, ethylene glycol tetraacetic acid
- GST, glutathione S-transferase
- Intra-molecular interaction
- RVH, recoverin homology
- RVHD, RVH domain
- TF, trigger factor
Collapse
Affiliation(s)
- Tatsuya Yamamoto
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
| | - Hiromichi Sakai
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
| | - Fumio Sakane
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
| |
Collapse
|
6
|
Li F, Yu T, Yu S. Structural dynamic and thermodynamic analysis of calcineurin B subunit induced by calcium/magnesium binding. Int J Biol Macromol 2013; 60:122-7. [DOI: 10.1016/j.ijbiomac.2013.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 05/10/2013] [Accepted: 05/13/2013] [Indexed: 10/26/2022]
|
7
|
Physical interaction between calcineurin and Cav3.2 T‐type Ca
2
+
channel modulates their functions. FEBS Lett 2013; 587:1723-30. [DOI: 10.1016/j.febslet.2013.04.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 04/26/2013] [Accepted: 04/29/2013] [Indexed: 11/23/2022]
|
8
|
Takahashi M, Yamamoto T, Sakai H, Sakane F. Calcium negatively regulates an intramolecular interaction between the N-terminal recoverin homology and EF-hand motif domains and the C-terminal C1 and catalytic domains of diacylglycerol kinase α. Biochem Biophys Res Commun 2012; 423:571-6. [PMID: 22695121 DOI: 10.1016/j.bbrc.2012.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 06/02/2012] [Indexed: 12/25/2022]
Abstract
The type I diacylglycerol kinase (DGK) isozymes (α, β and γ) contain a shared recoverin homology (RVH) domain, a tandem repeat of Ca2+-binding EF-hand motifs, two cysteine-rich C1 domains, and the catalytic domain. We previously reported that a DGKα mutant lacking the RVH domain and EF-hands was constitutively active, implying that the N-terminal region (NTR) of DGKα, consisting of the RVH domain and EF-hand motifs, intramolecularly interacts with and masks the activity of the C-terminal region (CTR), containing the C1 and catalytic domains. In this study, we demonstrate that a glutathione S-transferase (GST)-fused DGKα-NTR construct physically binds to a green fluorescent protein (GFP)-fused DGKα-CTR construct. Moreover, co-precipitation of GFP-DGKα-CTR with GST-DGKα-NTR was clearly attenuated by the addition of 1 μM Ca2+. This result indicates that Ca2+ induces dissociation of the physical interaction between DGKα-NTR and DGKα-CTR. In addition to previously reported calcium-dependent changes in the hydrophobicity and net surface charge, Ca2+ also appeared to induce a decrease in the α-helical content of DGKα-NTR. These results suggest that Ca2+-induced conformational changes in the NTR release the intramolecular association between the NTR and the CTR of DGKα.
Collapse
Affiliation(s)
- Masato Takahashi
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | | | | | | |
Collapse
|
9
|
Identification of the critical structural determinants of the EF-hand domain arrangements in calcium binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:608-19. [PMID: 22285364 DOI: 10.1016/j.bbapap.2012.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 12/02/2011] [Accepted: 01/04/2012] [Indexed: 11/22/2022]
Abstract
EF-hand calcium binding proteins (CaBPs) share strong sequence homology, but exhibit great diversity in structure and function. Thus although calmodulin (CaM) and calcineurin B (CNB) both consist of four EF hands, their domain arrangements are quite distinct. CaM and the CaM-like proteins are characterized by an extended architecture, whereas CNB and the CNB-like proteins have a more compact form. In this study, we performed structural alignments and molecular dynamics (MD) simulations on 3 CaM-like proteins and 6 CNB-like proteins, and quantified their distinct structural and dynamical features in an effort to establish how their sequences specify their structures and dynamics. Alignments of the EF2-EF3 region of these proteins revealed that several residues (not restricted to the linker between the EF2 and EF3 motifs) differed between the two groups of proteins. A customized inverse folding approach followed by structural assessments and MD simulations established the critical role of these residues in determining the structure of the proteins. Identification of the critical determinants of the two different EF-hand domain arrangements and the distinct dynamical features relevant to their respective functions provides insight into the relationships between sequence, structure, dynamics and function among these EF-hand CaBPs.
Collapse
|
10
|
|
11
|
Juvvadi PR, Fortwendel JR, Rogg LE, Burns KA, Randell SH, Steinbach WJ. Localization and activity of the calcineurin catalytic and regulatory subunit complex at the septum is essential for hyphal elongation and proper septation in Aspergillus fumigatus. Mol Microbiol 2011; 82:1235-59. [PMID: 22066998 DOI: 10.1111/j.1365-2958.2011.07886.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Calcineurin, a heterodimer composed of the catalytic (CnaA) and regulatory (CnaB) subunits, plays key roles in growth, virulence and stress responses of fungi. To investigate the contribution of CnaA and CnaB to hyphal growth and septation, ΔcnaB and ΔcnaAΔcnaB strains of Aspergillus fumigatus were constructed. CnaA colocalizes to the contractile actin ring early during septation and remains at the centre of the mature septum. While CnaB's septal localization is CnaA-dependent, CnaA's septal localization is CnaB-independent, but CnaB is required for CnaA's function at the septum. Catalytic null mutations in CnaA caused stunted growth despite septal localization of the calcineurin complex, indicating the requirement of calcineurin activity at the septum. Compared to the ΔcnaA and ΔcnaB strains, the ΔcnaAΔcnaB strain displayed more defective growth and aberrant septation. While three Ca(2+) -binding motifs in CnaB were sufficient for its association with CnaA at the septum, the amino-terminal arginine-rich domains (16-RRRR-19 and 44-RLRKR-48) are dispensable for septal localization, yet required for complete functionality. Mutation of the 51-KLDK-54 motif in CnaB causes its mislocalization from the septum to the nucleus, suggesting it is a nuclear export signal sequence. These findings confirm a cooperative role for the calcineurin complex in regulating hyphal growth and septation.
Collapse
Affiliation(s)
- Praveen Rao Juvvadi
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | | | | | | | | | | |
Collapse
|