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Fayez AG, Esmaiel NN, Ashaat EA, Refeat MM, Lotfy RS, Raouf HA, El Ruby MO. New drug-like small molecule antagonizes phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in patients with conotruncal heart defects. J Taibah Univ Med Sci 2023; 18:1244-1253. [PMID: 37250809 PMCID: PMC10213100 DOI: 10.1016/j.jtumed.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 02/02/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
Objectives Conotruncal heart defects (CTDs) are highly heritable, and approximately one-third of all congenital heart defects are due to CTDs. Through post-analysis of GWAS data relevant to CTDs, a new putative signal transduction pathway, called Vars2-Pic3ca-Akt, associated with CTD has been hypothesized. Here, we aimed to validate the Vars2-Pic3ca-Akt pathway experimentally by measuring Vars2 and PIP3 in patients with CTDs and controls, and to construct a PIP3 inhibitor, as one of harmful-relevant CTD pathogenesis, through an Akt-based drug design strategy. Methods rs2517582 genotype and relative Vars2 expression in 207 individuals were determined by DNA sequencing and qPCR respectively, and free plasma PIP3 in 190 individuals was quantified through ELISA. An Akt-pharmacophore feature model was used to discover PIP3 antagonists with multiple computational and drug-like estimation tools. Results CTD pathogenesis due to Vars2-Pic3ca-Akt overstimulation was confirmed by elevated Vars2 and PIP3 in patients with CTDs. We identified a new small molecule, 322PESB, that antagonizes PIP3 binding. This molecule was prioritized via virtual screening of 21 hypothetical small molecules and it showed minimal RMSD change, high binding affinity andlower dissociation constant than PIP3-Akt complex by 1.99 Kcal/Mol, thus resulting in an equilibrium shift toward 322PESB-Akt complex formation. Moreover, 322PESB exhibited acceptable pharmacokinetics and drug likeness features according to ADME and Lipinski's rule of five classifiers. This compound is the first potential drug-like molecule reported for patients with CTDs with elevated PIP3. Conclusion PIP3 is a useful diagnostic biomarker for patients with CTDs. The Akt-pharmacophore feature model is a feasible approach for discovery of PIP3 signalling antagonists. Further 322PESB development and testing are recommended.
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Affiliation(s)
- Alaaeldin G. Fayez
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Nora N. Esmaiel
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Engy A. Ashaat
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Miral M. Refeat
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Randa S. Lotfy
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Haiam Abdel Raouf
- Immunogenetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
| | - Mona O. El Ruby
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Giza, Egypt
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Sugiki T, Lee YH, Alsanousi N, Murata K, Kawamura I, Fujiwara T, Hanada K, Kojima C. A hybrid strategy combining solution NMR spectroscopy and isothermal titration calorimetry to characterize protein-nanodisc interaction. Anal Biochem 2021; 639:114521. [PMID: 34906540 DOI: 10.1016/j.ab.2021.114521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 11/19/2022]
Abstract
NMR is a powerful tool for characterizing intermolecular interactions at atomic resolution. However, the nature of the complex interactions of membrane-binding proteins makes it difficult to elucidate the interaction mechanisms. Here, we demonstrated that structural and thermodynamic analyses using solution NMR spectroscopy and isothermal titration calorimetry (ITC) can clearly detect a specific interaction between the pleckstrin homology (PH) domain of ceramide transport protein (CERT) and phosphatidylinositol 4-monophosphate (PI4P) embedded in the lipid nanodisc, and distinguish the specific interaction from nonspecific interactions with the bulk surface of the lipid nanodisc. This NMR-ITC hybrid strategy provides detailed characterization of protein-lipid membrane interactions.
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Affiliation(s)
- Toshihiko Sugiki
- Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan; Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungcheongbuk-do, 28119, South Korea; Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, South Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, South Korea
| | - Nesreen Alsanousi
- Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kaito Murata
- Graduate School of Engineering Science, Yokohama National University, Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kentaro Hanada
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan; Graduate School of Engineering Science, Yokohama National University, Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan.
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Nishimura T. A Real-Time Phosphatidylinositol 4-Phosphate 5-Kinase Assay Using Fluorescence Spectroscopy. Methods Mol Biol 2021; 2251:121-32. [PMID: 33481235 DOI: 10.1007/978-1-0716-1142-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Phosphatidylinositol 4-phosphate 5-kinase (PIP5K) is an enzyme that converts phosphatidylinositol 4-phosphate [PI4P] to phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. PIP5K plays a key role in the regulation of vesicular transport, cytoskeleton reorganization, and cell division. In general, to investigate an enzymatic activity of PIP5K, the amount of incorporated [P32] ATP into PI(4,5)P2 fraction is measured in in vitro reconstitution experiments. However, tools to monitor dynamic changes in its activity in real time have been lacking. Recently, we have developed a novel PIP5K assay using fluorescence spectroscopy. Compared to conventional methods in which lipids extraction steps are needed, our method is easy and quick to perform and enables a real-time analysis. This chapter provides a protocol to set up and perform the novel PIP5K assay we have recently established.
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Cash JN, Sharma PV, Tesmer JJ. Structural and biochemical characterization of the pleckstrin homology domain of the RhoGEF P-Rex2 and its regulation by PIP 3. J Struct Biol X 2018; 1:100001. [PMID: 34958187 PMCID: PMC7337056 DOI: 10.1016/j.yjsbx.2018.100001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 01/07/2023] Open
Abstract
P-Rex family Rho guanine-nucleotide exchange factors are important regulators of cell motility through their activation of a subset of small GTPases. Both P-Rex1 and P-Rex2 have also been implicated in the progression of certain cancers, including breast cancer and melanoma. Although these molecules display a high level of homology, differences exist in tissue distribution, physiological function, and regulation at the molecular level. Here, we sought to compare the P-Rex2 pleckstrin homology (PH) domain structure and ability to interact with PIP3 with those of P-Rex1. The 1.9 Å crystal structure of the P-Rex2 PH domain reveals conformational differences in the loop regions, yet biochemical studies indicate that the interaction of the P-Rex2 PH domain with PIP3 is very similar to that of P-Rex1. Binding of the PH domain to PIP3 is critical for P-Rex2 activity but not membrane localization, as previously demonstrated for P-Rex1. These studies serve as a starting point in the identification of P-Rex structural features that are divergent between isoforms and could be exploited for the design of P-Rex selective compounds.
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Key Words
- DEP, dishevelled, Egl-10, and pleckstrin
- DH, Dbl homology
- DSF, differential scanning fluorimetry
- DTT, dithiothreitol
- EDTA, ethylenediaminetetraacetic
- Gβγ, G protein β and γ subunits
- IP4P, inositol polyphosphate 4-phosphatase
- Ins(1,3,4,5)P4, inositol-1,3,4,5-tetrakisphosphate
- MBP, maltose binding protein
- P-Rex
- P-Rex, phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger
- PDZ, post-synaptic density protein, Drosophila disc large tumor suppressor, and zonula occludens-1 protein
- PH, pleckstrin homology
- PIP3, phosphatidylinositol 3,4,5-trisphosphate
- PMSF, phenylmethylsulfonyl fluoride
- PTEN, phosphatase and tensin homolog
- Phosphatidylinositol 3,4,5-trisphosphate
- Pleckstrin homology domain
- Rho guanine nucleotide exchange factor
- RhoGEF, Rho guanine-nucleotide exchange factor
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Affiliation(s)
- Jennifer N. Cash
- Department of Pharmacology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA,Department of Biological Chemistry, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Prateek V. Sharma
- Department of Pharmacology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA,Department of Biological Chemistry, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - John J.G. Tesmer
- Department of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47904, USA,Corresponding author.
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Rai S, Mohanty P, Bhatnagar S. Modeling, dynamics and phosphoinositide binding of the pleckstrin homology domain of two novel PLCs: η1 and η2. J Mol Graph Model 2018; 85:130-144. [PMID: 30193228 DOI: 10.1016/j.jmgm.2018.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 11/16/2022]
Abstract
PH domains mediate interactions involved in cell signaling, intracellular membrane transport regulation and cytoskeleton organization. Some PH domains bind phosphoinositides with different affinity and specificity. The two novel PLCη (1 and 2) possess an N-terminal PH domain (PHη1 and PHη2 respectively) that has been implicated in membrane association and induction of PLC activity. Understanding of the structure and dynamics is crucial for future modulation of lipid-protein interactions in PHη1, PHη2 and other PH domains. Therefore, the three-dimensional structure of PHη1 and PHη2 was modeled using ITASSER and phosphoinositides (IP3 and IP4) were docked in the inferred binding site using HADDOCK server. Molecular Dynamics simulations of unliganded and phosphoinositide bound PHη1 and PHη2 were performed using AMBER14 to study the mechanism of interaction, and conformational dynamics in response to phosphoinositide binding. The binding affinity was predicted using Kdeep server. The models of PHη1 and PHη2 had a conserved structural core consisting of seven β-strands and a C-terminal α-helix as seen in other PH domains. Sequence/structure analysis showed that phosphoinositide ligands bind PHη1 and PHη2 at the canonical binding site. Phosphoinositide binding induced movement of positively charged side chains towards the ligand, changes in the secondary structure especially at the β5-β6 loop and allosteric changes at the interface of β1-β2 and β5-β6 loops. Dynamics studies showed that the size of the binding site and differential affinity for IP3/IP4 binding is coordinated by the number, length, flexibility, secondary structure and allosteric interactions of the loops surrounding the phosphoinositide binding site.
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Affiliation(s)
- Sneha Rai
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India
| | - Pallavi Mohanty
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India.
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Riani YD, Matsuda T, Takemoto K, Nagai T. Green monomeric photosensitizing fluorescent protein for photo-inducible protein inactivation and cell ablation. BMC Biol 2018; 16:50. [PMID: 29712573 PMCID: PMC5928576 DOI: 10.1186/s12915-018-0514-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/06/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Photosensitizing fluorescent proteins, which generate reactive oxygen species (ROS) upon light irradiation, are useful for spatiotemporal protein inactivation and cell ablation. They give us clues about protein function, intracellular signaling pathways and intercellular interactions. Since ROS generation of a photosensitizer is specifically controlled by certain excitation wavelengths, utilizing colour variants of photosensitizing protein would allow multi-spatiotemporal control of inactivation. To expand the colour palette of photosensitizing protein, here we developed SuperNova Green from its red predecessor, SuperNova. RESULTS SuperNova Green is able to produce ROS spatiotemporally upon blue light irradiation. Based on protein characterization, SuperNova Green produces insignificant amounts of singlet oxygen and predominantly produces superoxide and its derivatives. We utilized SuperNova Green to specifically inactivate the pleckstrin homology domain of phospholipase C-δ1 and to ablate cancer cells in vitro. As a proof of concept for multi-spatiotemporal control of inactivation, we demonstrate that SuperNova Green can be used with its red variant, SuperNova, to perform independent protein inactivation or cell ablation studies in a spatiotemporal manner by selective light irradiation. CONCLUSION Development of SuperNova Green has expanded the photosensitizing protein toolbox to optogenetically control protein inactivation and cell ablation.
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Affiliation(s)
- Yemima Dani Riani
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Tomoki Matsuda
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan.,The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Osaka, Ibaraki, 567-0047, Japan
| | - Kiwamu Takemoto
- Graduate School of Medicine, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, 236-0027, Japan
| | - Takeharu Nagai
- Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan. .,The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Osaka, Ibaraki, 567-0047, Japan.
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Berberich H, Terwesten F, Rakow S, Sahu P, Bouchard C, Meixner M, Philipsen S, Kolb P, Bauer UM. Identification and in silico structural analysis of Gallus gallus protein arginine methyltransferase 4 (PRMT4). FEBS Open Bio 2017; 7:1909-1923. [PMID: 29226078 PMCID: PMC5715347 DOI: 10.1002/2211-5463.12323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/25/2017] [Indexed: 12/13/2022] Open
Abstract
Protein arginine methyltransferase 4 (PRMT4) is an essential epigenetic regulator of fundamental and conserved processes during vertebrate development, such as pluripotency and differentiation. Surprisingly, PRMT4 homologs have been identified in nearly all vertebrate classes except the avian genome. This raises the possibility that in birds PRMT4 functions are taken over by other PRMT family members. Here, we reveal the existence of a bona fidePRMT4 homolog in the chicken, Gallus gallus. Using a biochemical approach, we initially purified a putative chicken PRMT4 protein and thus provided the first evidence for the presence of an endogenous PRMT4‐specific enzymatic activity toward histone H3 arginine 17 (H3R17) in avian cells. We then isolated a G. gallus PRMT4 (ggPRMT4) transcript encompassing the complete open reading frame. Recombinant ggPRMT4 possesses intrinsic methyltransferase activity toward H3R17. CRISPR/Cas9‐mediated deletion of ggPRMT4 demonstrated that the transcript identified here encodes avian PRMT4. Combining protein–protein docking and homology modeling based on published crystal structures of murine PRMT4, we found a strong structural similarity of the catalytic core domain between chicken and mammalian PRMT4. Strikingly, in silico structural comparison of the N‐terminal Pleckstrin homology (PH) domain of avian and murine PRMT4 identified strictly conserved amino acids that are involved in an interaction interface toward the catalytic core domain, facilitating for the first time a prediction of the relative spatial arrangement of these two domains. Our novel findings are particularly exciting in light of the essential function of the PH domain in substrate recognition and methylation by PRMT4.
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Affiliation(s)
- Hannah Berberich
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
| | - Felix Terwesten
- Institute of Pharmaceutical Chemistry Philipps-University Marburg Germany
| | - Sinja Rakow
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
| | - Peeyush Sahu
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
| | - Caroline Bouchard
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
| | - Marion Meixner
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
| | - Sjaak Philipsen
- Department of Cell Biology Erasmus MC Rotterdam The Netherlands
| | - Peter Kolb
- Institute of Pharmaceutical Chemistry Philipps-University Marburg Germany
| | - Uta-Maria Bauer
- Institute of Molecular Biology and Tumor Research (IMT) Philipps-University Marburg Germany
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Ackermann MA, King B, Lieberman NAP, Bobbili PJ, Rudloff M, Berndsen CE, Wright NT, Hecker PA, Kontrogianni-Konstantopoulos A. Novel obscurins mediate cardiomyocyte adhesion and size via the PI3K/AKT/mTOR signaling pathway. J Mol Cell Cardiol 2017; 111:27-39. [PMID: 28826662 DOI: 10.1016/j.yjmcc.2017.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 12/29/2022]
Abstract
The intercalated disc of cardiac muscle embodies a highly-ordered, multifunctional network, essential for the synchronous contraction of the heart. Over 200 known proteins localize to the intercalated disc. The challenge now lies in their characterization as it relates to the coupling of neighboring cells and whole heart function. Using molecular, biochemical and imaging techniques, we characterized for the first time two small obscurin isoforms, obscurin-40 and obscurin-80, which are enriched at distinct locations of the intercalated disc. Both proteins bind specifically and directly to select phospholipids via their pleckstrin homology (PH) domain. Overexpression of either isoform or the PH-domain in cardiomyocytes results in decreased cell adhesion and size via reduced activation of the PI3K/AKT/mTOR pathway that is intimately linked to cardiac hypertrophy. In addition, obscurin-80 and obscurin-40 are significantly reduced in acute (myocardial infarction) and chronic (pressure overload) murine cardiac-stress models underscoring their key role in maintaining cardiac homeostasis. Our novel findings implicate small obscurins in the maintenance of cardiomyocyte size and coupling, and the development of heart failure by antagonizing the PI3K/AKT/mTOR pathway.
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Hardie RC, Liu CH, Randall AS, Sengupta S. In vivo tracking of phosphoinositides in Drosophila photoreceptors. J Cell Sci 2015; 128:4328-40. [PMID: 26483384 PMCID: PMC4712823 DOI: 10.1242/jcs.180364] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/12/2015] [Indexed: 01/26/2023] Open
Abstract
In order to monitor phosphoinositide turnover during phospholipase C (PLC)-mediated Drosophila phototransduction, fluorescently tagged lipid probes were expressed in photoreceptors and imaged both in dissociated cells, and in eyes of intact living flies. Of six probes tested, Tb(R332H) (a mutant of the Tubby protein pleckstrin homology domain) was judged the best reporter for phosphatidylinositol (4,5)-bisphosphate [PtdIns(4,5)P2], and the P4M domain from Legionella SidM for phosphatidylinositol 4-phosphate (PtdIns4P). Using accurately calibrated illumination, we found that only ∼50% of PtdIns(4,5)P2 and very little PtdIns4P were depleted by full daylight intensities in wild-type flies, but both were severely depleted by ∼100-fold dimmer intensities in mutants lacking Ca(2+)-permeable transient receptor potential (TRP) channels or protein kinase C (PKC). Resynthesis of PtdIns4P (t½ ∼12 s) was faster than PtdIns(4,5)P2 (t½ ∼40 s), but both were greatly slowed in mutants of DAG kinase (rdgA) or PtdIns transfer protein (rdgB). The results indicate that Ca(2+)- and PKC-dependent inhibition of PLC is required for enabling photoreceptors to maintain phosphoinositide levels despite high rates of hydrolysis by PLC, and suggest that phosphorylation of PtdIns4P to PtdIns(4,5)P2 is the rate-limiting step of the cycle.
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Affiliation(s)
- Roger C Hardie
- Department of Physiology Development and Neuroscience, Cambridge University, Cambridge CB2 3EG, UK
| | - Che-Hsiung Liu
- Department of Physiology Development and Neuroscience, Cambridge University, Cambridge CB2 3EG, UK
| | - Alexander S Randall
- Department of Physiology Development and Neuroscience, Cambridge University, Cambridge CB2 3EG, UK
| | - Sukanya Sengupta
- Department of Physiology Development and Neuroscience, Cambridge University, Cambridge CB2 3EG, UK
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Smith EM, Hennen J, Chen Y, Mueller JD. Z-scan fluorescence profile deconvolution of cytosolic and membrane-associated protein populations. Anal Biochem 2015; 480:11-20. [PMID: 25862080 DOI: 10.1016/j.ab.2015.03.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/22/2015] [Accepted: 03/23/2015] [Indexed: 12/30/2022]
Abstract
This study introduces a technique that characterizes the spatial distribution of peripheral membrane proteins that associate reversibly with the plasma membrane. An axial scan through the cell generates a z-scan intensity profile of a fluorescently labeled peripheral membrane protein. This profile is analytically separated into membrane and cytoplasmic components by accounting for both the cell geometry and the point spread function. We experimentally validated the technique and characterized both the resolvability and stability of z-scan measurements. Furthermore, using the cellular brightness of green fluorescent protein, we were able to convert the fluorescence intensities into concentrations at the membrane and in the cytoplasm. We applied the technique to study the translocation of the pleckstrin homology domain of phospholipase C delta 1 labeled with green fluorescent protein on ionomycin treatment. Analysis of the z-scan fluorescence profiles revealed protein-specific cell height changes and allowed for comparison between the observed fluorescence changes and predictions based on the cellular surface area-to-volume ratio. The quantitative capability of z-scan fluorescence profile deconvolution offers opportunities for investigating peripheral membrane proteins in the living cell that were previously not accessible.
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Affiliation(s)
- Elizabeth M Smith
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jared Hennen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yan Chen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joachim D Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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Spellmann I, Rujescu D, Musil R, Meyerwas S, Giegling I, Genius J, Zill P, Dehning S, Cerovecki A, Seemüller F, Schennach R, Hartmann AM, Schäfer M, Müller N, Möller HJ, Riedel M. Pleckstrin homology domain containing 6 protein (PLEKHA6) polymorphisms are associated with psychopathology and response to treatment in schizophrenic patients. Prog Neuropsychopharmacol Biol Psychiatry 2014; 51:190-5. [PMID: 24576533 DOI: 10.1016/j.pnpbp.2014.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 02/13/2014] [Accepted: 02/18/2014] [Indexed: 12/21/2022]
Abstract
Pleckstrin homology domain (PH domain) comprises approximately 120 amino acids and is integrated in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton. This domain can bind phosphatidylinositol (3,4,5)-triphosphate and phosphatidylinositol (4,5)-biphosphate and proteins such as the βγ-subunits of heterotrimeric G proteins and protein kinase C. Associations with psychiatric diseases have not been investigated yet. To identify genes involved in response to antipsychotics, mice were treated with haloperidol (1mg/kg, n = 11) or saline (n = 12) for one week. By analyzing microarray data, we observed an increase of pleckstrin homology domain containing 6 (PLEKHA6) gene expression. Furthermore, we genotyped 263 schizophrenic patients, who were treated monotherapeutically with different antipsychotics within randomized-controlled trials. Psychopathology was measured weekly using the PANSS for a minimum of four and a maximum of twelve weeks. Correlations between PANSS subscale scores at baseline and PANSS improvement scores after four weeks of treatment and genotypes were calculated by using a linear model for all investigated SNPs. We found associations between four PLEKHA6 polymorphisms (rs17333933 (T/G), rs3126209 (C/T), rs4951338 (A/G) and rs100900571 (T/C)) and different PANSS subscales at baseline. Furthermore two different polymorphisms (rs7513240 (T/C), rs4951353 (A/G)) were found to be associated with therapy response in terms of a significant correlation with different PANSS improvement subscores after four weeks of antipsychotic treatment. Our observation of an association between genetic polymorphisms of a protein of the PH domain and psychopathology data in schizophrenic patients might be indicative for an involvement of PLEKHA6 in the pathophysiology of schizophrenia and the therapy response towards antipsychotics.
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Affiliation(s)
- Ilja Spellmann
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Bezirkskrankenhaus Kaufbeuren, Department of Psychiatry and Psychotherapy.
| | - Dan Rujescu
- Martin Luther University of Halle (Saale), Department of Psychiatry and Psychotherapy
| | - Richard Musil
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Bezirkskrankenhaus Kaufbeuren, Department of Psychiatry and Psychotherapy
| | | | - Ina Giegling
- Martin Luther University of Halle (Saale), Department of Psychiatry and Psychotherapy
| | - Just Genius
- LVR-Hospital Essen, Department of Psychiatry and Psychotherapy
| | - Peter Zill
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Bezirkskrankenhaus Kaufbeuren, Department of Psychiatry and Psychotherapy
| | - Sandra Dehning
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Bezirkskrankenhaus Kaufbeuren, Department of Psychiatry and Psychotherapy
| | - Anja Cerovecki
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Bezirkskrankenhaus Kaufbeuren, Department of Psychiatry and Psychotherapy
| | - Florian Seemüller
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Bezirkskrankenhaus Kaufbeuren, Department of Psychiatry and Psychotherapy
| | - Rebecca Schennach
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Bezirkskrankenhaus Kaufbeuren, Department of Psychiatry and Psychotherapy
| | - Annette M Hartmann
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Bezirkskrankenhaus Kaufbeuren, Department of Psychiatry and Psychotherapy
| | - Martin Schäfer
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Bezirkskrankenhaus Kaufbeuren, Department of Psychiatry and Psychotherapy
| | - Norbert Müller
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Bezirkskrankenhaus Kaufbeuren, Department of Psychiatry and Psychotherapy
| | - Hans-Jürgen Möller
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Bezirkskrankenhaus Kaufbeuren, Department of Psychiatry and Psychotherapy
| | - Michael Riedel
- Ludwig Maximilians University of Munich, Department of Psychiatry and Psychotherapy and Vinzenz-von-Paul-Hospital Rottweil
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Kim Y, Yoon Y. Elucidation of different inhibition mechanism of small chemicals on PtdInsP-binding domains using in silico docking experiments. Bioorg Med Chem Lett 2014; 24:2256-62. [PMID: 24736117 DOI: 10.1016/j.bmcl.2014.03.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 03/24/2014] [Accepted: 03/26/2014] [Indexed: 10/25/2022]
Abstract
Phosphatidylinositides, most negatively charged lipids in cellular membranes, regulate diverse effector proteins through the interaction with their lipid binding domains. We have previously reported inhibitory effect of small chemicals on the interaction between PtdIns(3,4,5)P3 and Btk PH domain. Here, we report that the inhibitory effects of same sets of chemicals on Grp1 PH domain and epsin1 ENTH domain to elucidate diversity of inhibitory mechanisms upon different lipid binding domains. Among the chemicals, chemical 8 showed best inhibition in vitro assay for Grp1 PH domain and epsin1 ENTH domain, and then the interaction between small chemicals and lipid binding domains was further investigated by in silico docking experiments. As a result, it was concluded that the diverse inhibitory effects on different lipid binding domains were dependent on not only the number of interactions between small chemical and domain, but also additional interaction with positively charged surfaces as the secondary binding sites. This finding will help to develop lipid binding inhibitors as antagonists for lipid-protein interactions, and these inhibitors would be novel therapeutic drug candidates via regulating effector proteins involved in severe human diseases.
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