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Article: A Fluorescence-Based Sensor for Calibrated Measurement of Protein Kinase Stability in Live Cells.

Paul, Joseph W / Muratcioğlu, Serena / Kuriyan, John

bioRxiv : the preprint server for biology

2023

Abstract: Oncogenic mutations can destabilize signaling proteins, resulting in increased or unregulated activity. Thus, there is considerable interest in mapping the relationship between mutations and the stability of proteins, to better understand the ... ...

Abstract	Oncogenic mutations can destabilize signaling proteins, resulting in increased or unregulated activity. Thus, there is considerable interest in mapping the relationship between mutations and the stability of proteins, to better understand the consequences of oncogenic mutations and potentially inform the development of new therapeutics. Here, we develop a tool to study protein-kinase stability in live mammalian cells and the effects of the HSP90 chaperone system on the stability of these kinases. We monitor the fluorescence of kinases fused to a fluorescent protein relative to that of a co-expressed reference fluorescent protein. We used this tool to study the dependence of Src- and Raf-family kinases on the HSP90 system. We demonstrate that this sensor reports on destabilization induced by oncogenic mutations in these kinases. We also show that Src-homology 2 (SH2) and Src-homology 3 (SH3) domains, which are required for autoinhibition of Src-family kinases, stabilize these kinase domains in the cell. Our expression-calibrated sensor enables the facile characterization of the effects of mutations and small-molecule drugs on protein-kinase stability.
Language	English
Publishing date	2023-12-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.07.570636
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Article ; Online: Flexible linkers in CaMKII control the balance between activating and inhibitory autophosphorylation.

Bhattacharyya, Moitrayee / Lee, Young Kwang / Muratcioglu, Serena / Qiu, Baiyu / Nyayapati, Priya / Schulman, Howard / Groves, Jay T / Kuriyan, John

eLife

2020 Volume 9

Abstract: The many variants of human ... ...

Abstract	The many variants of human Ca
MeSH term(s)	Calcium/metabolism ; Calcium-Calmodulin-Dependent Protein Kinase Type 2/antagonists & inhibitors ; Calcium-Calmodulin-Dependent Protein Kinase Type 2/chemistry ; Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism ; Calmodulin/metabolism ; Catalytic Domain ; Enzyme Activation ; Humans ; Phosphorylation ; Protein Isoforms ; Single Molecule Imaging
Chemical Substances	Calmodulin ; Protein Isoforms ; CAMK2A protein, human (EC 2.7.11.17) ; CAMK2B protein, human (EC 2.7.11.17) ; Calcium-Calmodulin-Dependent Protein Kinase Type 2 (EC 2.7.11.17) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2020-03-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.53670
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Article ; Online: PDEδ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization.

Muratcioglu, Serena / Jang, Hyunbum / Gursoy, Attila / Keskin, Ozlem / Nussinov, Ruth

The journal of physical chemistry. B

2017 Volume 121, Issue 24, Page(s) 5917–5927

Abstract: To signal, Ras isoforms must be enriched at the plasma membrane (PM). It was suggested that phosphodiesterase-δ (PDEδ) can bind and shuttle some farnesylated Ras isoforms to the PM, but not all. Among these, interest focused on K-Ras4B, the most abundant ...

Abstract	To signal, Ras isoforms must be enriched at the plasma membrane (PM). It was suggested that phosphodiesterase-δ (PDEδ) can bind and shuttle some farnesylated Ras isoforms to the PM, but not all. Among these, interest focused on K-Ras4B, the most abundant oncogenic Ras isoform. To study PDEδ/Ras interactions, we modeled and simulated the PDEδ/K-Ras4B complex. We obtained structures, which were similar to two subsequently determined crystal structures. We next modeled and simulated complexes of PDEδ with the farnesylated hypervariable regions of K-Ras4A and N-Ras. Earlier data suggested that PDEδ extracts K-Ras4B and N-Ras from the PM, but surprisingly not K-Ras4A. Earlier analysis of the crystal structures advanced that the presence of large/charged residues adjacent to the farnesylated site precludes the PDEδ interaction. Here, we show that PDEδ can bind to farnesylated K-Ras4A and N-Ras like K-Ras4B, albeit not as strongly. This weaker binding, coupled with the stronger anchoring of K-Ras4A in the membrane (but not of electrostatically neutral N-Ras), can explain the observation why PDEδ is unable to effectively extract K-Ras4A. We thus propose that farnesylated Ras isoforms can bind PDEδ to fulfill the required PM enrichment, and argue that the different environments, PM versus solution, can resolve apparently puzzling Ras observations. These are novel insights that would not be expected based on the crystal structures alone, which provide an elegant rationale for previously puzzling observations of the differential effects of PDEδ on farnesylated Ras family proteins.
MeSH term(s)	Cell Membrane/metabolism ; Cyclic Nucleotide Phosphodiesterases, Type 6/chemistry ; Cyclic Nucleotide Phosphodiesterases, Type 6/metabolism ; Humans ; Molecular Dynamics Simulation ; Protein Isoforms ; Protein Transport ; Proto-Oncogene Proteins p21(ras)/chemistry ; Proto-Oncogene Proteins p21(ras)/metabolism
Chemical Substances	Protein Isoforms ; Cyclic Nucleotide Phosphodiesterases, Type 6 (EC 3.1.4.35) ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2)
Language	English
Publishing date	2017-06-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.7b03035
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Article ; Online: Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers.

Jang, Hyunbum / Muratcioglu, Serena / Gursoy, Attila / Keskin, Ozlem / Nussinov, Ruth

The Biochemical journal

2016 Volume 473, Issue 12, Page(s) 1719–1732

Abstract: Are the dimer structures of active Ras isoforms similar? This question is significant since Ras can activate its effectors as a monomer; however, as a dimer, it promotes Raf's activation and MAPK (mitogen-activated protein kinase) cell signalling. In the ...

Abstract	Are the dimer structures of active Ras isoforms similar? This question is significant since Ras can activate its effectors as a monomer; however, as a dimer, it promotes Raf's activation and MAPK (mitogen-activated protein kinase) cell signalling. In the present study, we model possible catalytic domain dimer interfaces of membrane-anchored GTP-bound K-Ras4B and H-Ras, and compare their conformations. The active helical dimers formed by the allosteric lobe are isoform-specific: K-Ras4B-GTP favours the α3 and α4 interface; H-Ras-GTP favours α4 and α5. Both isoforms also populate a stable β-sheet dimer interface formed by the effector lobe; a less stable β-sandwich interface is sustained by salt bridges of the β-sheet side chains. Raf's high-affinity β-sheet interaction is promoted by the active helical interface. Collectively, Ras isoforms' dimer conformations are not uniform; instead, the isoform-specific dimers reflect the favoured interactions of the HVRs (hypervariable regions) with cell membrane microdomains, biasing the effector-binding site orientations, thus isoform binding selectivity.
MeSH term(s)	Amino Acid Sequence ; Cysteine/chemistry ; Cysteine/metabolism ; Humans ; Lipoproteins/chemistry ; Lipoproteins/genetics ; Lipoproteins/metabolism ; Mitogen-Activated Protein Kinases/genetics ; Mitogen-Activated Protein Kinases/metabolism ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Protein Binding ; Protein Isoforms/chemistry ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Protein Multimerization/genetics ; Protein Multimerization/physiology ; Protein Structure, Secondary ; Signal Transduction/genetics ; Signal Transduction/physiology ; ras Proteins/chemistry ; ras Proteins/genetics ; ras Proteins/metabolism
Chemical Substances	Lipoproteins ; Protein Isoforms ; Mitogen-Activated Protein Kinases (EC 2.7.11.24) ; ras Proteins (EC 3.6.5.2) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2016-04-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BCJ20160031
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Article: PDEÎ´ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization

Muratcioglu, Serena / Jang Hyunbum / Gursoy Attila / Keskin Ozlem / Nussinov Ruth

Journal of physical chemistry. 2017 June 22, v. 121, no. 24

2017

Abstract: To signal, Ras isoforms must be enriched at the plasma membrane (PM). It was suggested that phosphodiesterase-Î´ (PDEÎ´) can bind and shuttle some farnesylated Ras isoforms to the PM, but not all. Among these, interest focused on K-Ras4B, the most ... ...

Abstract	To signal, Ras isoforms must be enriched at the plasma membrane (PM). It was suggested that phosphodiesterase-Î´ (PDEÎ´) can bind and shuttle some farnesylated Ras isoforms to the PM, but not all. Among these, interest focused on K-Ras4B, the most abundant oncogenic Ras isoform. To study PDEÎ´/Ras interactions, we modeled and simulated the PDEÎ´/K-Ras4B complex. We obtained structures, which were similar to two subsequently determined crystal structures. We next modeled and simulated complexes of PDEÎ´ with the farnesylated hypervariable regions of K-Ras4A and N-Ras. Earlier data suggested that PDEÎ´ extracts K-Ras4B and N-Ras from the PM, but surprisingly not K-Ras4A. Earlier analysis of the crystal structures advanced that the presence of large/charged residues adjacent to the farnesylated site precludes the PDEÎ´ interaction. Here, we show that PDEÎ´ can bind to farnesylated K-Ras4A and N-Ras like K-Ras4B, albeit not as strongly. This weaker binding, coupled with the stronger anchoring of K-Ras4A in the membrane (but not of electrostatically neutral N-Ras), can explain the observation why PDEÎ´ is unable to effectively extract K-Ras4A. We thus propose that farnesylated Ras isoforms can bind PDEÎ´ to fulfill the required PM enrichment, and argue that the different environments, PM versus solution, can resolve apparently puzzling Ras observations. These are novel insights that would not be expected based on the crystal structures alone, which provide an elegant rationale for previously puzzling observations of the differential effects of PDEÎ´ on farnesylated Ras family proteins.
Keywords	crystal structure ; plasma membrane ; proteins
Language	English
Dates of publication	2017-0622
Size	p. 5917-5927.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021%2Facs.jpcb.7b03035
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Flexible linkers in CaMKII control the balance between activating and inhibitory autophosphorylation

Moitrayee Bhattacharyya / Young Kwang Lee / Serena Muratcioglu / Baiyu Qiu / Priya Nyayapati / Howard Schulman / Jay T Groves / John Kuriyan

eLife, Vol

2020 Volume 9

Abstract: The many variants of human Ca2+/calmodulin-dependent protein kinase II (CaMKII) differ in the lengths and sequences of disordered linkers connecting the kinase domains to the oligomeric hubs of the holoenzyme. CaMKII activity depends on the balance ... ...

Abstract	The many variants of human Ca2+/calmodulin-dependent protein kinase II (CaMKII) differ in the lengths and sequences of disordered linkers connecting the kinase domains to the oligomeric hubs of the holoenzyme. CaMKII activity depends on the balance between activating and inhibitory autophosphorylation (on Thr 286 and Thr 305/306, respectively, in the human α isoform). Variation in the linkers could alter transphosphorylation rates within a holoenzyme and the balance of autophosphorylation outcomes. We show, using mammalian cell expression and a single-molecule assay, that the balance of autophosphorylation is flipped between CaMKII variants with longer and shorter linkers. For the principal isoforms in the brain, CaMKII-α, with a ~30 residue linker, readily acquires activating autophosphorylation, while CaMKII-β, with a ~200 residue linker, is biased towards inhibitory autophosphorylation. Our results show how the responsiveness of CaMKII holoenzymes to calcium signals can be tuned by varying the relative levels of isoforms with long and short linkers.
Keywords	single-molecule microscopy ; CaMKII isoforms ; autophosphorylation ; flexible linker ; phosphatase resistance ; kinase activity ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
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Article ; Online: Advances in template-based protein docking by utilizing interfaces towards completing structural interactome.

Muratcioglu, Serena / Guven-Maiorov, Emine / Keskin, Özlem / Gursoy, Attila

Current opinion in structural biology

2015 Volume 35, Page(s) 87–92

Abstract: The increase in the number of structurally determined protein complexes strengthens template-based docking (TBD) methods for modelling protein-protein interactions (PPIs). These methods utilize the known structures of protein complexes as templates to ... ...

Abstract	The increase in the number of structurally determined protein complexes strengthens template-based docking (TBD) methods for modelling protein-protein interactions (PPIs). These methods utilize the known structures of protein complexes as templates to predict the quaternary structure of the target proteins. The templates may be partial or complete structures. Interface based (partial) methods have recently gained interest due in part to the observation that the interface regions are reusable. We describe how available template interfaces can be used to obtain the structural models of protein interactions. Despite the agreement that a majority of the protein complexes can be modelled using the available Protein Data Bank (PDB) structures, a handful of studies argue that we need more template proteins to increase the structural coverage of PPIs. We also discuss the performance of the interface TBD methods at large scale, and the significance of capturing multiple conformations for improving accuracy.
MeSH term(s)	Molecular Docking Simulation/methods ; Protein Interaction Mapping/methods ; Proteins/chemistry ; Proteins/metabolism
Chemical Substances	Proteins
Language	English
Publishing date	2015-12
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2015.10.001
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Article ; Online: Breakage of the oligomeric CaMKII hub by the regulatory segment of the kinase.

Karandur, Deepti / Bhattacharyya, Moitrayee / Xia, Zijie / Lee, Young Kwang / Muratcioglu, Serena / McAffee, Darren / McSpadden, Ethan D / Qiu, Baiyu / Groves, Jay T / Williams, Evan R / Kuriyan, John

eLife

2020 Volume 9

Abstract: ... ...

Abstract	Ca
MeSH term(s)	Calcium-Calmodulin-Dependent Protein Kinase Type 2/antagonists & inhibitors ; Escherichia coli ; HEK293 Cells ; Holoenzymes/metabolism ; Humans ; Molecular Dynamics Simulation ; Phosphorylation ; Proteins/genetics ; Proteins/metabolism ; Signal Transduction/genetics
Chemical Substances	CAMK2N1 protein, human ; Holoenzymes ; Proteins ; Calcium-Calmodulin-Dependent Protein Kinase Type 2 (EC 2.7.11.17)
Language	English
Publishing date	2020-09-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.57784
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Article ; Online: Ras Conformational Ensembles, Allostery, and Signaling.

Lu, Shaoyong / Jang, Hyunbum / Muratcioglu, Serena / Gursoy, Attila / Keskin, Ozlem / Nussinov, Ruth / Zhang, Jian

Chemical reviews

2016 Volume 116, Issue 11, Page(s) 6607–6665

Abstract: Ras proteins are classical members of small GTPases that function as molecular switches by alternating between inactive GDP-bound and active GTP-bound states. Ras activation is regulated by guanine nucleotide exchange factors that catalyze the exchange ... ...

Abstract	Ras proteins are classical members of small GTPases that function as molecular switches by alternating between inactive GDP-bound and active GTP-bound states. Ras activation is regulated by guanine nucleotide exchange factors that catalyze the exchange of GDP by GTP, and inactivation is terminated by GTPase-activating proteins that accelerate the intrinsic GTP hydrolysis rate by orders of magnitude. In this review, we focus on data that have accumulated over the past few years pertaining to the conformational ensembles and the allosteric regulation of Ras proteins and their interpretation from our conformational landscape standpoint. The Ras ensemble embodies all states, including the ligand-bound conformations, the activated (or inactivated) allosteric modulated states, post-translationally modified states, mutational states, transition states, and nonfunctional states serving as a reservoir for emerging functions. The ensemble is shifted by distinct mutational events, cofactors, post-translational modifications, and different membrane compositions. A better understanding of Ras biology can contribute to therapeutic strategies.
MeSH term(s)	Allosteric Regulation ; Catalytic Domain ; Guanosine Triphosphate/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Protein Structure, Tertiary ; Signal Transduction/physiology ; ras Proteins/chemistry ; ras Proteins/metabolism
Chemical Substances	Guanosine Triphosphate (86-01-1) ; ras Proteins (EC 3.6.5.2)
Language	English
Publishing date	2016--08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/acs.chemrev.5b00542
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Article ; Online: Beyond the heterodimer model for mineralocorticoid and glucocorticoid receptor interactions in nuclei and at DNA.

Pooley, John R / Rivers, Caroline A / Kilcooley, Michael T / Paul, Susana N / Cavga, Ayse Derya / Kershaw, Yvonne M / Muratcioglu, Serena / Gursoy, Attila / Keskin, Ozlem / Lightman, Stafford L

PloS one

2020 Volume 15, Issue 1, Page(s) e0227520

Abstract: Glucocorticoid (GR) and mineralocorticoid receptors (MR) are believed to classically bind DNA as homodimers or MR-GR heterodimers to influence gene regulation in response to pulsatile basal or stress-evoked glucocorticoid secretion. Pulsed corticosterone ...

Abstract	Glucocorticoid (GR) and mineralocorticoid receptors (MR) are believed to classically bind DNA as homodimers or MR-GR heterodimers to influence gene regulation in response to pulsatile basal or stress-evoked glucocorticoid secretion. Pulsed corticosterone presentation reveals MR and GR co-occupy DNA only at the peaks of glucocorticoid oscillations, allowing interaction. GR DNA occupancy was pulsatile, while MR DNA occupancy was prolonged through the inter-pulse interval. In mouse mammary 3617 cells MR-GR interacted in the nucleus and at a chromatin-associated DNA binding site. Interactions occurred irrespective of ligand type and receptors formed complexes of higher order than heterodimers. We also detected MR-GR interactions ex-vivo in rat hippocampus. An expanded range of MR-GR interactions predicts structural allostery allowing a variety of transcriptional outcomes and is applicable to the multiple tissue types that co-express both receptors in the same cells whether activated by the same or different hormones.
MeSH term(s)	Allosteric Regulation ; Amino Acid Sequence ; Animals ; Binding Sites ; Cell Line ; Cell Nucleus/metabolism ; Chromatin/metabolism ; Corticosterone/pharmacology ; DNA/chemistry ; DNA/metabolism ; Dimerization ; Hippocampus/metabolism ; Male ; Protein Interaction Domains and Motifs/drug effects ; Protein Structure, Quaternary ; Rats ; Rats, Sprague-Dawley ; Receptors, Glucocorticoid/chemistry ; Receptors, Glucocorticoid/genetics ; Receptors, Glucocorticoid/metabolism ; Receptors, Mineralocorticoid/chemistry ; Receptors, Mineralocorticoid/genetics ; Receptors, Mineralocorticoid/metabolism ; Sequence Alignment ; Ultradian Rhythm
Chemical Substances	Chromatin ; Receptors, Glucocorticoid ; Receptors, Mineralocorticoid ; DNA (9007-49-2) ; Corticosterone (W980KJ009P)
Language	English
Publishing date	2020-01-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0227520
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