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Article ; Online: A direct fluorometric activity assay for lipid kinases and phosphatases.

Sun, Jiachen / Singaram, Indira / Soflaee, Mona Hoseini / Cho, Wonhwa

2020 Volume 61, Issue 6, Page(s) 945–952

Abstract: Lipid kinases and phosphatases play key roles in cell signaling and regulation, are implicated in many human diseases, and are thus attractive targets for drug development. Currently, no direct in vitro activity assay is available for these important ... ...

Abstract	Lipid kinases and phosphatases play key roles in cell signaling and regulation, are implicated in many human diseases, and are thus attractive targets for drug development. Currently, no direct in vitro activity assay is available for these important enzymes, which hampers mechanistic studies as well as high-throughput screening of small molecule modulators. Here, we report a highly sensitive and quantitative assay employing a ratiometric fluorescence sensor that directly and specifically monitors the real-time concentration change of a single lipid species. Because of its modular design, the assay system can be applied to a wide variety of lipid kinases and phosphatases, including class I phosphoinositide 3-kinase (PI3K) and phosphatase and tensin homolog (PTEN). When applied to PI3K, the assay provided detailed mechanistic information about the product inhibition and substrate acyl-chain selectivity of PI3K and enabled rapid evaluation of small molecule inhibitors. We also used this assay to quantitatively determine the substrate specificity of PTEN, providing new insight into its physiological function. In summary, we have developed a fluorescence-based real-time assay for PI3K and PTEN that we anticipate could be adapted to measure the activities of other lipid kinases and phosphatases with high sensitivity and accuracy.
MeSH term(s)	Enzyme Assays/methods ; Fluorometry ; Phosphoric Monoester Hydrolases/metabolism ; Phosphotransferases (Alcohol Group Acceptor)/metabolism ; Substrate Specificity
Chemical Substances	Phosphotransferases (Alcohol Group Acceptor) (EC 2.7.1.-) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
Language	English
Publishing date	2020-04-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80154-9
ISSN	1539-7262 ; 0022-2275
ISSN (online)	1539-7262
ISSN	0022-2275
DOI	10.1194/jlr.D120000794
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Article ; Online: Development of a novel spatiotemporal depletion system for cellular cholesterol.

Pham, Ha / Singaram, Indira / Sun, Jiachen / Ralko, Arthur / Puckett, Madalyn / Sharma, Ashutosh / Vrielink, Alice / Cho, Wonhwa

Journal of lipid research

2022 Volume 63, Issue 3, Page(s) 100178

Abstract: Cholesterol is an essential component of mammalian cell membranes whose subcellular concentration and function are tightly regulated by de novo biosynthesis, transport, and storage. Although recent reports have suggested diverse functions of cellular ... ...

Abstract	Cholesterol is an essential component of mammalian cell membranes whose subcellular concentration and function are tightly regulated by de novo biosynthesis, transport, and storage. Although recent reports have suggested diverse functions of cellular cholesterol in different subcellular membranes, systematic investigation of its site-specific roles has been hampered by the lack of a methodology for spatiotemporal manipulation of cellular cholesterol levels. Here, we report the development of a new cholesterol depletion system that allows for spatiotemporal manipulation of intracellular cholesterol levels. This system utilizes a genetically encoded cholesterol oxidase whose intrinsic membrane binding activity is engineered in such a way that its membrane targeting can be controlled in a spatiotemporally specific manner via chemically induced dimerization. In combination with in situ quantitative imaging of cholesterol and signaling activity measurements, this system allows for unambiguous determination of site-specific functions of cholesterol in different membranes, including the plasma membrane and the lysosomal membrane.
MeSH term(s)	Animals ; Cell Membrane/metabolism ; Cholesterol/metabolism ; Endosomes/metabolism ; Intracellular Membranes/metabolism ; Lysosomes/metabolism ; Mammals/metabolism
Chemical Substances	Cholesterol (97C5T2UQ7J)
Language	English
Publishing date	2022-02-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80154-9
ISSN	1539-7262 ; 0022-2275
ISSN (online)	1539-7262
ISSN	0022-2275
DOI	10.1016/j.jlr.2022.100178
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Article: PI(3,5)P

Sun, Jiachen / Song, Seohyeon / Singaram, Indira / Sharma, Ashutosh / Wang, Wei / Hu, Yusi / Lo, Wen-Ting / Koch, Philipp Alexander / Zhao, Jean J / Haucke, Volker / Gao, Ruixuan / Cho, Wonhwa

bioRxiv : the preprint server for biology

2023

Abstract: 3'-Phosphoinositides are ubiquitous cellular lipids that play pivotal regulatory roles in health and disease. Generation of 3'-phosphoinositides are driven by three families of phosphoinositide 3-kinases (PI3K) but the mechanisms underlying their ... ...

Abstract	3'-Phosphoinositides are ubiquitous cellular lipids that play pivotal regulatory roles in health and disease. Generation of 3'-phosphoinositides are driven by three families of phosphoinositide 3-kinases (PI3K) but the mechanisms underlying their regulation and cross-talk are not fully understood. Among 3'-phosphoinositides, phosphatidylinositol-3,5-bisphosphate (PI(3,5)P
Language	English
Publishing date	2023-01-25
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.25.525550
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Article ; Online: Photostable and Orthogonal Solvatochromic Fluorophores for Simultaneous

Sharma, Ashutosh / Sun, Jiachen / Singaram, Indira / Ralko, Arthur / Lee, Daesung / Cho, Wonhwa

ACS chemical biology

2020 Volume 15, Issue 7, Page(s) 1913–1920

Abstract: Ratiometric fluorescence sensors are powerful tools for direct quantification of diverse biological analytes. To overcome a shortage of solvatochromic fluorophores crucial ... ...

Abstract	Ratiometric fluorescence sensors are powerful tools for direct quantification of diverse biological analytes. To overcome a shortage of solvatochromic fluorophores crucial for
MeSH term(s)	Animals ; Fluorenes/chemical synthesis ; Fluorenes/chemistry ; Fluorescent Dyes/chemical synthesis ; Fluorescent Dyes/chemistry ; Mice ; NIH 3T3 Cells ; Phosphatidylinositol Phosphates/analysis ; Small Molecule Libraries/chemical synthesis ; Small Molecule Libraries/chemistry ; Spectrometry, Fluorescence
Chemical Substances	Fluorenes ; Fluorescent Dyes ; Phosphatidylinositol Phosphates ; Small Molecule Libraries ; phosphatidylinositol 3,4,5-triphosphate
Language	English
Publishing date	2020-06-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.0c00241
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Article ; Online: Structure and Dynamics of Membrane Proteins and Membrane Associated Proteins with Native Bicelles from Eukaryotic Tissues.

Smrt, Sean T / Draney, Adrian W / Singaram, Indira / Lorieau, Justin L

Biochemistry

2017 Volume 56, Issue 40, Page(s) 5318–5327

Abstract: In vitro studies of protein structure, function, and dynamics typically preclude the complex range of molecular interactions found in living tissues. In vivo studies elucidate these complex relationships, yet they are typically incompatible with the ... ...

Abstract	In vitro studies of protein structure, function, and dynamics typically preclude the complex range of molecular interactions found in living tissues. In vivo studies elucidate these complex relationships, yet they are typically incompatible with the extensive and controlled biophysical experiments available in vitro. We present an alternative approach by extracting membranes from eukaryotic tissues to produce native bicelles to capture the rich and complex molecular environment of in vivo studies while retaining the advantages of in vitro experiments. Native bicelles derived from chicken egg or mouse cerebrum tissues contain a rich composition of phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylserine (PS), phosphatidylinositol (PI), phosphatidic acid (PA), lysolipids, cholesterol, ceramides (CM), and sphingomyelin (SM). The bicelles also contain source-specific lipids such as triacylglycerides (TAGs) and sulfatides from egg and brain tissues, respectively. With the influenza hemagglutinin fusion peptide (HAfp) and the C-terminal Src homology domain of lymphocyte-specific protein-tyrosine kinase (lck-cSH2), we show that membrane proteins and membrane associated proteins reconstituted in native bicelles produce high-resolution NMR data and probe native protein-lipid interactions.
MeSH term(s)	Animals ; Cell Membrane/chemistry ; Cell Membrane/metabolism ; Membrane Lipids/chemistry ; Membrane Lipids/metabolism ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Mice ; Micelles ; Models, Molecular ; Protein Conformation
Chemical Substances	Membrane Lipids ; Membrane Proteins ; Micelles
Language	English
Publishing date	2017-10-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.7b00575
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Article ; Online: Targeting lipid-protein interaction to treat Syk-mediated acute myeloid leukemia.

Singaram, Indira / Sharma, Ashutosh / Pant, Shashank / Lihan, Muyun / Park, Mi-Jeong / Pergande, Melissa / Buwaneka, Pawanthi / Hu, Yusi / Mahmud, Nadim / Kim, You-Me / Cologna, Stephanie / Gevorgyan, Vladimir / Khan, Irum / Tajkhorshid, Emad / Cho, Wonhwa

Nature chemical biology

2022 Volume 19, Issue 2, Page(s) 239–250

Abstract: Membrane lipids control the cellular activity of kinases containing the Src homology 2 (SH2) domain through direct lipid-SH2 domain interactions. Here we report development of new nonlipidic small molecule inhibitors of the lipid-SH2 domain interaction ... ...

Abstract	Membrane lipids control the cellular activity of kinases containing the Src homology 2 (SH2) domain through direct lipid-SH2 domain interactions. Here we report development of new nonlipidic small molecule inhibitors of the lipid-SH2 domain interaction that block the cellular activity of their host proteins. As a pilot study, we evaluated the efficacy of lipid-SH2 domain interaction inhibitors for spleen tyrosine kinase (Syk), which is implicated in hematopoietic malignancies, including acute myeloid leukemia (AML). An optimized inhibitor (WC36) specifically and potently suppressed oncogenic activities of Syk in AML cell lines and patient-derived AML cells. Unlike ATP-competitive Syk inhibitors, WC36 was refractory to de novo and acquired drug resistance due to its ability to block not only the Syk kinase activity, but also its noncatalytic scaffolding function that is linked to drug resistance. Collectively, our study shows that targeting lipid-protein interaction is a powerful approach to developing new small molecule drugs.
MeSH term(s)	Humans ; Protein-Tyrosine Kinases/metabolism ; Intracellular Signaling Peptides and Proteins/metabolism ; Pilot Projects ; src Homology Domains ; Phosphorylation ; Leukemia, Myeloid, Acute/drug therapy ; Lipids ; Syk Kinase/metabolism
Chemical Substances	Protein-Tyrosine Kinases (EC 2.7.10.1) ; Intracellular Signaling Peptides and Proteins ; Lipids ; SYK protein, human (EC 2.7.10.2) ; Syk Kinase (EC 2.7.10.2)
Language	English
Publishing date	2022-10-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2202962-X
ISSN	1552-4469 ; 1552-4450
ISSN (online)	1552-4469
ISSN	1552-4450
DOI	10.1038/s41589-022-01150-z
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Zs.A 6251: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
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Article: Structure and Dynamics of Membrane Proteins and Membrane Associated Proteins with Native Bicelles from Eukaryotic Tissues

Smrt, Sean T / Draney Adrian W / Lorieau Justin L / Singaram Indira

Biochemistry. 2017 Oct. 10, v. 56, no. 40

2017

Abstract	In vitro studies of protein structure, function, and dynamics typically preclude the complex range of molecular interactions found in living tissues. In vivo studies elucidate these complex relationships, yet they are typically incompatible with the extensive and controlled biophysical experiments available in vitro. We present an alternative approach by extracting membranes from eukaryotic tissues to produce native bicelles to capture the rich and complex molecular environment of in vivo studies while retaining the advantages of in vitro experiments. Native bicelles derived from chicken egg or mouse cerebrum tissues contain a rich composition of phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylserine (PS), phosphatidylinositol (PI), phosphatidic acid (PA), lysolipids, cholesterol, ceramides (CM), and sphingomyelin (SM). The bicelles also contain source-specific lipids such as triacylglycerides (TAGs) and sulfatides from egg and brain tissues, respectively. With the influenza hemagglutinin fusion peptide (HAfp) and the C-terminal Src homology domain of lymphocyte-specific protein-tyrosine kinase (lck-cSH2), we show that membrane proteins and membrane associated proteins reconstituted in native bicelles produce high-resolution NMR data and probe native proteinâlipid interactions.
Keywords	ceramides ; cerebrum ; cholesterol ; eggs ; hemagglutinins ; in vitro studies ; in vivo studies ; influenza ; membrane proteins ; mice ; nuclear magnetic resonance spectroscopy ; phosphatidylcholines ; phosphatidylethanolamines ; phosphatidylserines ; protein structure ; sequence homology ; sphingomyelins ; triacylglycerols
Language	English
Dates of publication	2017-1010
Size	p. 5318-5327.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021%2Facs.biochem.7b00575
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Article ; Online: Cellular phosphatase activity of C1-Ten/Tensin2 is controlled by Phosphatidylinositol-3,4,5-triphosphate binding through the C1-Ten/Tensin2 SH2 domain.

Kim, Eui / Kim, Do-Hyeon / Singaram, Indira / Jeong, Heeyoon / Koh, Ara / Lee, Jiyoun / Cho, Wonhwa / Ryu, Sung Ho

Cellular signalling

2018 Volume 51, Page(s) 130–138

Abstract: Regulation of tyrosine phosphorylation on insulin receptor substrate-1 (IRS-1) is essential for insulin signaling. The protein tyrosine phosphatase (PTP) C1-Ten/Tensin2 has been implicated in the regulation of IRS-1, but the molecular basis of this ... ...

Abstract	Regulation of tyrosine phosphorylation on insulin receptor substrate-1 (IRS-1) is essential for insulin signaling. The protein tyrosine phosphatase (PTP) C1-Ten/Tensin2 has been implicated in the regulation of IRS-1, but the molecular basis of this dephosphorylation is not fully understood. Here, we demonstrate that the cellular phosphatase activity of C1-Ten/Tensin2 on IRS-1 is mediated by the binding of the C1-Ten/Tensin2 Src-homology 2 (SH2) domain to phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,5)P
MeSH term(s)	Animals ; Escherichia coli ; HEK293 Cells ; Humans ; Insulin Receptor Substrate Proteins/metabolism ; L Cells ; Mice ; Mutagenesis, Site-Directed ; Phosphatidylinositol 3-Kinases/metabolism ; Phosphatidylinositol Phosphates/metabolism ; Phosphorylation ; Phosphotyrosine/metabolism ; Tensins/chemistry ; Tensins/genetics ; Tensins/metabolism ; src Homology Domains
Chemical Substances	Insulin Receptor Substrate Proteins ; Phosphatidylinositol Phosphates ; Tensins ; phosphatidylinositol 3,4,5-triphosphate ; Phosphotyrosine (21820-51-9) ; TNS2 protein, human (EC 3.1.3.-)
Language	English
Publishing date	2018-08-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1002702-6
ISSN	1873-3913 ; 0898-6568
ISSN (online)	1873-3913
ISSN	0898-6568
DOI	10.1016/j.cellsig.2018.07.009
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Article ; Online: α-Catenin homodimers are recruited to phosphoinositide-activated membranes to promote adhesion.

Wood, Megan N / Ishiyama, Noboru / Singaram, Indira / Chung, Connie M / Flozak, Annette S / Yemelyanov, Alex / Ikura, Mitsu / Cho, Wonhwa / Gottardi, Cara J

The Journal of cell biology

2017 Volume 216, Issue 11, Page(s) 3767–3783

Abstract: A unique feature of α-catenin localized outside the cadherin-catenin complex is its capacity to form homodimers, but the subcellular localization and functions of this form of α-catenin remain incompletely understood. We identified a cadherin-free form ... ...

Abstract	A unique feature of α-catenin localized outside the cadherin-catenin complex is its capacity to form homodimers, but the subcellular localization and functions of this form of α-catenin remain incompletely understood. We identified a cadherin-free form of α-catenin that is recruited to the leading edge of migrating cells in a phosphatidylinositol 3-kinase-dependent manner. Surface plasmon resonance analysis shows that α-catenin homodimers, but not monomers, selectively bind phosphatidylinositol-3,4,5-trisphosphate-containing lipid vesicles with high affinity, where three basic residues, K488, K493, and R496, contribute to binding. Chemical-induced dimerization of α-catenin containing a synthetic dimerization domain promotes its accumulation within lamellipodia and elaboration of protrusions with extended filopodia, which are attenuated in the α-catenin
MeSH term(s)	Animals ; Cell Adhesion ; Cell Line, Tumor ; Cell Membrane/metabolism ; Cell Movement ; Dogs ; Epithelial Cells/metabolism ; Humans ; Madin Darby Canine Kidney Cells ; Mutation ; Phosphatidylinositol 3-Kinase/metabolism ; Phosphatidylinositol Phosphates/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Pseudopodia/metabolism ; Signal Transduction ; Time Factors ; Transfection ; alpha Catenin/genetics ; alpha Catenin/metabolism
Chemical Substances	Phosphatidylinositol Phosphates ; alpha Catenin ; phosphatidylinositol 3,4,5-triphosphate ; Phosphatidylinositol 3-Kinase (EC 2.7.1.137)
Language	English
Publishing date	2017-09-05
Publishing country	United States
Document type	Journal Article ; Video-Audio Media ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.201612006
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Article: Quantitative Lipid Imaging Reveals a New Signaling Function of Phosphatidylinositol-3,4-Bisphophate: Isoform- and Site-Specific Activation of Akt

Liu, Shu-Lin / Wang, Zhi-Gang / Hu, Yusi / Xin, Yao / Singaram, Indira / Gorai, Sukhamoy / Zhou, Xin / Shim, Yoonjung / Min, Jung-Hyun / Gong, Liang-Wei / Hay, Nissim / Zhang, Jin / Cho, Wonhwa

Molecular cell. 2018 Sept. 20, v. 71, no. 6

2018

Abstract: Activation of class I phosphatidylinositol 3-kinase (PI3K) leads to formation of phosphatidylinositol-3,4,5-trisphophate (PIP3) and phosphatidylinositol-3,4-bisphophate (PI34P2), which spatiotemporally coordinate and regulate a myriad of cellular ... ...

Abstract	Activation of class I phosphatidylinositol 3-kinase (PI3K) leads to formation of phosphatidylinositol-3,4,5-trisphophate (PIP3) and phosphatidylinositol-3,4-bisphophate (PI34P2), which spatiotemporally coordinate and regulate a myriad of cellular processes. By simultaneous quantitative imaging of PIP3 and PI34P2 in live cells, we here show that they have a distinctively different spatiotemporal distribution and history in response to growth factor stimulation, which allows them to selectively induce the membrane recruitment and activation of Akt isoforms. PI34P2 selectively activates Akt2 at both the plasma membrane and early endosomes, whereas PIP3 selectively stimulates Akt1 and Akt3 exclusively at the plasma membrane. These spatiotemporally distinct activation patterns of Akt isoforms provide a mechanism for their differential regulation of downstream signaling molecules. Collectively, our studies show that different spatiotemporal dynamics of PIP3 and PI34P2 and their ability to selectively activate key signaling proteins allow them to mediate class I PI3K signaling pathways in a spatiotemporally specific manner.
Keywords	endosomes ; image analysis ; lipids ; phosphatidylinositol 3-kinase ; plasma membrane ; proteins ; signal transduction
Language	English
Dates of publication	2018-0920
Size	p. 1092-1104.e5.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2018.07.035
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