1
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McCombs AM, Armendariz JR, Falke JJ. Ras signaling mechanisms: New insights from single-molecule biophysics. Biophys J 2024:S0006-3495(24)00591-5. [PMID: 39217418 DOI: 10.1016/j.bpj.2024.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/23/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024] Open
Affiliation(s)
- Anne Marie McCombs
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, Colorado
| | - Joy R Armendariz
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, Colorado
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, Colorado.
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2
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Chon NL, Tran S, Miller CS, Lin H, Knight JD. A conserved electrostatic membrane-binding surface in synaptotagmin-like proteins revealed using molecular phylogenetic analysis and homology modeling. Protein Sci 2024; 33:e4850. [PMID: 38038838 PMCID: PMC10731544 DOI: 10.1002/pro.4850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/29/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Protein structure prediction has emerged as a core technology for understanding biomolecules and their interactions. Here, we combine homology-based structure prediction with molecular phylogenetic analysis to study the evolution of electrostatic membrane binding among the vertebrate synaptotagmin-like protein (Slp) family. Slp family proteins play key roles in the membrane trafficking of large dense-core secretory vesicles. Our previous experimental and computational study found that the C2A domain of Slp-4 (also called granuphilin) binds with high affinity to anionic phospholipids in the cytoplasmic leaflet of the plasma membrane through a large positively charged protein surface centered on a cluster of phosphoinositide-binding lysine residues. Because this surface contributes greatly to Slp-4 C2A domain membrane binding, we hypothesized that the net charge on the surface might be evolutionarily conserved. To test this hypothesis, the known C2A sequences of Slp-4 among vertebrates were organized by class (from mammalia to pisces) using molecular phylogenetic analysis. Consensus sequences for each class were then identified and used to generate homology structures, from which Poisson-Boltzmann electrostatic potentials were calculated. For comparison, homology structures and electrostatic potentials were also calculated for the five human Slp protein family members. The results demonstrate that the charge on the membrane-binding surface is highly conserved throughout the evolution of Slp-4, and more highly conserved than many individual residues among the human Slp family paralogs. Such molecular phylogenetic-driven computational analysis can help to describe the evolution of electrostatic interactions between proteins and membranes which are crucial for their function.
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Affiliation(s)
- Nara L. Chon
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Sherleen Tran
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | | | - Hai Lin
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
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3
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Yu J, Boehr DD. Regulatory mechanisms triggered by enzyme interactions with lipid membrane surfaces. Front Mol Biosci 2023; 10:1306483. [PMID: 38099197 PMCID: PMC10720463 DOI: 10.3389/fmolb.2023.1306483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Recruitment of enzymes to intracellular membranes often modulates their catalytic activity, which can be important in cell signaling and membrane trafficking. Thus, re-localization is not only important for these enzymes to gain access to their substrates, but membrane interactions often allosterically regulate enzyme function by inducing conformational changes across different time and amplitude scales. Recent structural, biophysical and computational studies have revealed how key enzymes interact with lipid membrane surfaces, and how this membrane binding regulates protein structure and function. This review summarizes the recent progress in understanding regulatory mechanisms involved in enzyme-membrane interactions.
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Affiliation(s)
| | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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4
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Gordon MT, Ziemba BP, Falke JJ. PDK1:PKCα heterodimer association-dissociation dynamics in single-molecule diffusion tracks on a target membrane. Biophys J 2023; 122:2301-2310. [PMID: 36733254 PMCID: PMC10257113 DOI: 10.1016/j.bpj.2023.01.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Previous studies have documented the formation of a heterodimer between the two protein kinases PDK1 and PKCα on a lipid bilayer containing their target lipids. This work investigates the association-dissociation kinetics of this PDK1:PKCα heterodimer. The approach monitors the two-dimensional diffusion of single, membrane-associated PDK1 molecules for diffusivity changes as PKCα molecules bind and unbind. In the absence of PKCα, a membrane-associated PDK1 molecule exhibits high diffusivity (or large diffusion constant, D) because its membrane-contacting PH domain binds the target PIP3 lipid headgroup with little bilayer penetration, yielding minimal frictional drag against the bilayer. In contrast, membrane-associated PKCα contacts the bilayer via its C1A, C1B, and C2 domains, which each bind at least one target lipid with significant bilayer insertion, yielding a large frictional drag and low diffusivity. The present findings reveal that individual fluor-PDK1 molecules freely diffusing on the membrane surface undergo reversible switching between distinct high and low diffusivity states, corresponding to the PDK1 monomer and the PDK1:PKCα heterodimer, respectively. The observed single-molecule diffusion trajectories are converted to step length time courses, then subjected to two-state, hidden Markov modeling and dwell time analysis. The findings reveal that both the PDK1 monomer state and the PDK1:PKCα heterodimer state decay via simple exponential kinetics, yielding estimates of rate constants for state switching in both directions. Notably, the PDK1:PKCα heterodimer has been shown to competitively inhibit PDK1 phosphoactivation of AKT1, and is believed to play a tumor suppressor role by limiting excess activation of the highly oncogenic PDK1/AKT1/mTOR pathway. Thus, the present elucidation of the PDK1:PKCα association-dissociation kinetics has important biological and medical implications. More broadly, the findings illustrate the power of single-molecule diffusion measurements to reveal the kinetics of association-dissociation events in membrane signaling reactions that yield a large change in diffusive mobility.
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Affiliation(s)
- Moshe T Gordon
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, Colorado
| | - Brian P Ziemba
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, Colorado
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, Colorado.
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5
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Fan W, Ren W, Liu C. Advances in optical counting and imaging of micro/nano single-entity reactors for biomolecular analysis. Anal Bioanal Chem 2023; 415:97-117. [PMID: 36322160 PMCID: PMC9628437 DOI: 10.1007/s00216-022-04395-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022]
Abstract
Ultrasensitive detection of biomarkers is of paramount importance in various fields. Superior to the conventional ensemble measurement-based assays, single-entity assays, especially single-entity detection-based digital assays, not only can reach ultrahigh sensitivity, but also possess the potential to examine the heterogeneities among the individual target molecules within a population. In this review, we summarized the current biomolecular analysis methods that based on optical counting and imaging of the micro/nano-sized single entities that act as the individual reactors (e.g., micro-/nanoparticles, microemulsions, and microwells). We categorize the corresponding techniques as analog and digital single-entity assays and provide detailed information such as the design principles, the analytical performance, and their implementation in biomarker analysis in this work. We have also set critical comments on each technique from these aspects. At last, we reflect on the advantages and limitations of the optical single-entity counting and imaging methods for biomolecular assay and highlight future opportunities in this field.
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Affiliation(s)
- Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi’an, 710119 Shaanxi Province People’s Republic of China ,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi’an, 710119 Shaanxi Province People’s Republic of China ,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an, 710119 Shaanxi Province People’s Republic of China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi’an, 710119 Shaanxi Province People’s Republic of China ,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi’an, 710119 Shaanxi Province People’s Republic of China ,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an, 710119 Shaanxi Province People’s Republic of China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi’an, 710119 Shaanxi Province People’s Republic of China ,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi’an, 710119 Shaanxi Province People’s Republic of China ,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an, 710119 Shaanxi Province People’s Republic of China
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6
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Black JD, Affandi T, Black AR, Reyland ME. PKCα and PKCδ: Friends and Rivals. J Biol Chem 2022; 298:102194. [PMID: 35760100 PMCID: PMC9352922 DOI: 10.1016/j.jbc.2022.102194] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 01/06/2023] Open
Abstract
PKC comprises a large family of serine/threonine kinases that share a requirement for allosteric activation by lipids. While PKC isoforms have significant homology, functional divergence is evident among subfamilies and between individual PKC isoforms within a subfamily. Here, we highlight these differences by comparing the regulation and function of representative PKC isoforms from the conventional (PKCα) and novel (PKCδ) subfamilies. We discuss how unique structural features of PKCα and PKCδ underlie differences in activation and highlight the similar, divergent, and even opposing biological functions of these kinases. We also consider how PKCα and PKCδ can contribute to pathophysiological conditions and discuss challenges to targeting these kinases therapeutically.
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Affiliation(s)
- Jennifer D Black
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE.
| | - Trisiani Affandi
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus
| | - Adrian R Black
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE
| | - Mary E Reyland
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus.
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7
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Katti SS, Krieger IV, Ann J, Lee J, Sacchettini JC, Igumenova TI. Structural anatomy of Protein Kinase C C1 domain interactions with diacylglycerol and other agonists. Nat Commun 2022; 13:2695. [PMID: 35577811 PMCID: PMC9110374 DOI: 10.1038/s41467-022-30389-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/28/2022] [Indexed: 11/22/2022] Open
Abstract
Diacylglycerol (DAG) is a versatile lipid whose 1,2-sn-stereoisomer serves both as second messenger in signal transduction pathways that control vital cellular processes, and as metabolic precursor for downstream signaling lipids such as phosphatidic acid. Effector proteins translocate to available DAG pools in the membranes by using conserved homology 1 (C1) domains as DAG-sensing modules. Yet, how C1 domains recognize and capture DAG in the complex environment of a biological membrane has remained unresolved for the 40 years since the discovery of Protein Kinase C (PKC) as the first member of the DAG effector cohort. Herein, we report the high-resolution crystal structures of a C1 domain (C1B from PKCδ) complexed to DAG and to each of four potent PKC agonists that produce different biological readouts and that command intense therapeutic interest. This structural information details the mechanisms of stereospecific recognition of DAG by the C1 domains, the functional properties of the lipid-binding site, and the identities of the key residues required for the recognition and capture of DAG and exogenous agonists. Moreover, the structures of the five C1 domain complexes provide the high-resolution guides for the design of agents that modulate the activities of DAG effector proteins.
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Affiliation(s)
- Sachin S. Katti
- grid.264756.40000 0004 4687 2082Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840 USA
| | - Inna V. Krieger
- grid.264756.40000 0004 4687 2082Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840 USA
| | - Jihyae Ann
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Jeewoo Lee
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - James C. Sacchettini
- grid.264756.40000 0004 4687 2082Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840 USA
| | - Tatyana I. Igumenova
- grid.264756.40000 0004 4687 2082Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840 USA
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8
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Baffi TR, Newton AC. Protein kinase C: release from quarantine by mTORC2. Trends Biochem Sci 2022; 47:518-530. [DOI: 10.1016/j.tibs.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 01/31/2023]
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9
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Gordon MT, Ziemba BP, Falke JJ. Single-molecule studies reveal regulatory interactions between master kinases PDK1, AKT1, and PKC. Biophys J 2021; 120:5657-5673. [PMID: 34673053 DOI: 10.1016/j.bpj.2021.10.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/30/2021] [Accepted: 10/13/2021] [Indexed: 12/26/2022] Open
Abstract
Leukocyte migration is controlled by a leading-edge chemosensory pathway that generates the regulatory lipid phosphatidylinositol-3,4,5-trisphosphate (PIP3), a growth signal, thereby driving leading-edge expansion up attractant gradients toward sites of infection, inflammation, or tissue damage. PIP3 also serves as an important growth signal in growing cells and oncogenesis. The kinases PDK1, AKT1 or PKB, and PKCα are key components of a plasma-membrane-based PIP3 and Ca2+ signaling circuit that regulates these processes. PDK1 and AKT1 are recruited to the membrane by PIP3, whereas PKCα is recruited to the membrane by Ca2+. All three of these master kinases phosphoregulate an array of protein targets. For example, PDK1 activates AKT1, PKCα, and other AGC kinases by phosphorylation at key sites. PDK1 is believed to form PDK1-AKT1 and PDK1-PKCα heterodimers stabilized by a PDK1-interacting fragment (PIF) interaction between the PDK1 PIF pocket and the PIF motif of the AGC binding partner. Here, we present the first, to our knowledge, single-molecule studies of full-length PDK1 and AKT1 on target membrane surfaces, as well as their interaction with full-length PKCα. These studies directly detect membrane-bound PDK1-AKT1 and PDK1-PKCα heterodimers stabilized by PIF interactions formed at physiological ligand concentrations. PKCα exhibits eightfold higher PDK1 affinity than AKT1 and can competitively displace AKT1 from PDK1-AKT1 heterodimers. Ensemble activity measurements under matched conditions reveal that PDK1 activates AKT1 via a cis mechanism by phosphorylating an AKT1 molecule in the same PDK1-AKT1 heterodimer, whereas PKCα acts as a competitive inhibitor of this phosphoactivation reaction by displacing AKT1 from PDK1. Overall, the findings provide insights into the binding and regulatory interactions of the three master kinases on their target membrane and suggest that a recently described tumor suppressor activity of PKC isoforms may arise from its ability to downregulate PDK1-AKT1 phosphoactivation in the PIP3-PDK1-AKT1-mTOR pathway linked to cell growth and oncogenesis.
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Affiliation(s)
- Moshe T Gordon
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, Colorado
| | - Brian P Ziemba
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, Colorado
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, Colorado.
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10
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Baffi TR, Lordén G, Wozniak JM, Feichtner A, Yeung W, Kornev AP, King CC, Del Rio JC, Limaye AJ, Bogomolovas J, Gould CM, Chen J, Kennedy EJ, Kannan N, Gonzalez DJ, Stefan E, Taylor SS, Newton AC. mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif. Sci Signal 2021; 14:eabe4509. [PMID: 33850054 PMCID: PMC8208635 DOI: 10.1126/scisignal.abe4509] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The complex mTORC2 is accepted to be the kinase that controls the phosphorylation of the hydrophobic motif, a key regulatory switch for AGC kinases, although whether mTOR directly phosphorylates this motif remains controversial. Here, we identified an mTOR-mediated phosphorylation site that we termed the TOR interaction motif (TIM; F-x3-F-pT), which controls the phosphorylation of the hydrophobic motif of PKC and Akt and the activity of these kinases. The TIM is invariant in mTORC2-dependent AGC kinases, is evolutionarily conserved, and coevolved with mTORC2 components. Mutation of this motif in Akt1 and PKCβII abolished cellular kinase activity by impairing activation loop and hydrophobic motif phosphorylation. mTORC2 directly phosphorylated the PKC TIM in vitro, and this phosphorylation event was detected in mouse brain. Overexpression of PDK1 in mTORC2-deficient cells rescued hydrophobic motif phosphorylation of PKC and Akt by a mechanism dependent on their intrinsic catalytic activity, revealing that mTORC2 facilitates the PDK1 phosphorylation step, which, in turn, enables autophosphorylation. Structural analysis revealed that PKC homodimerization is driven by a TIM-containing helix, and biophysical proximity assays showed that newly synthesized, unphosphorylated PKC dimerizes in cells. Furthermore, disruption of the dimer interface by stapled peptides promoted hydrophobic motif phosphorylation. Our data support a model in which mTORC2 relieves nascent PKC dimerization through TIM phosphorylation, recruiting PDK1 to phosphorylate the activation loop and triggering intramolecular hydrophobic motif autophosphorylation. Identification of TIM phosphorylation and its role in the regulation of PKC provides the basis for AGC kinase regulation by mTORC2.
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Affiliation(s)
- Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gema Lordén
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Charles C King
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jason C Del Rio
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ameya J Limaye
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Julius Bogomolovas
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Christine M Gould
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ju Chen
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Susan S Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.
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11
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The G-Protein Rab5A Activates VPS34 Complex II, a Class III PI3K, by a Dual Regulatory Mechanism. Biophys J 2020; 119:2205-2218. [PMID: 33137306 DOI: 10.1016/j.bpj.2020.10.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/04/2020] [Accepted: 10/07/2020] [Indexed: 02/07/2023] Open
Abstract
VPS34 complex II (VPS34CII) is a 386-kDa assembly of the lipid kinase subunit VPS34 and three regulatory subunits that altogether function as a prototypical class III phosphatidylinositol-3-kinase (PI3K). When the active VPS34CII complex is docked to the cytoplasmic surface of endosomal membranes, it phosphorylates its substrate lipid (phosphatidylinositol, PI) to generate the essential signaling lipid phosphatidylinositol-3-phosphate (PI3P). In turn, PI3P recruits an array of signaling proteins containing PI3P-specific targeting domains (including FYVE, PX, and PROPPINS) to the membrane surface, where they initiate key cell processes. In endocytosis and early endosome development, net VPS34CII-catalyzed PI3P production is greatly amplified by Rab5A, a small G protein of the Ras GTPase superfamily. Moreover, VPS34CII and Rab5A are each strongly linked to multiple human diseases. Thus, a molecular understanding of the mechanism by which Rab5A activates lipid kinase activity will have broad impacts in both signaling biology and medicine. Two general mechanistic models have been proposed for small G protein activation of PI3K lipid kinases. 1) In the membrane recruitment mechanism, G protein association increases the density of active kinase on the membrane. And 2) in the allosteric activation mechanism, G protein allosterically triggers an increase in the specific activity (turnover rate) of the membrane-bound kinase molecule. This study employs an in vitro single-molecule approach to elucidate the mechanism of GTP-Rab5A-associated VPS34CII kinase activation in a reconstituted GTP-Rab5A-VPS34CII-PI3P-PX signaling pathway on a target membrane surface. The findings reveal that both membrane recruitment and allosteric mechanisms make important contributions to the large increase in VPS34CII kinase activity and PI3P production triggered by membrane-anchored GTP-Rab5A. Notably, under near-physiological conditions in the absence of other activators, membrane-anchored GTP-Rab5A provides strong, virtually binary on-off switching and is required for VPS34CII membrane binding and PI3P production.
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12
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Rapid exposure of macrophages to drugs resolves four classes of effects on the leading edge sensory pseudopod: Non-perturbing, adaptive, disruptive, and activating. PLoS One 2020; 15:e0233012. [PMID: 32469878 PMCID: PMC7259666 DOI: 10.1371/journal.pone.0233012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/26/2020] [Indexed: 11/19/2022] Open
Abstract
Leukocyte migration is controlled by a membrane-based chemosensory pathway on the leading edge pseudopod that guides cell movement up attractant gradients during the innate immune and inflammatory responses. This study employed single cell and population imaging to investigate drug-induced perturbations of leading edge pseudopod morphology in cultured, polarized RAW macrophages. The drugs tested included representative therapeutics (acetylsalicylic acid, diclofenac, ibuprofen, acetaminophen) as well as control drugs (PDGF, Gö6976, wortmannin). Notably, slow addition of any of the four therapeutics to cultured macrophages, mimicking the slowly increasing plasma concentration reported for standard oral dosage in patients, yielded no detectable change in pseudopod morphology. This finding is consistent with the well established clinical safety of these drugs. However, rapid drug addition to cultured macrophages revealed four distinct classes of effects on the leading edge pseudopod: (i) non-perturbing drug exposures yielded no detectable change in pseudopod morphology (acetylsalicylic acid, diclofenac); (ii) adaptive exposures yielded temporary collapse of the extended pseudopod and its signature PI(3,4,5)P3 lipid signal followed by slow recovery of extended pseudopod morphology (ibuprofen, acetaminophen); (iii) disruptive exposures yielded long-term pseudopod collapse (Gö6976, wortmannin); and (iv) activating exposures yielded pseudopod expansion (PDGF). The novel observation of adaptive exposures leads us to hypothesize that rapid addition of an adaptive drug overwhelms an intrinsic or extrinsic adaptation system yielding temporary collapse followed by adaptive recovery, while slow addition enables gradual adaptation to counteract the drug perturbation in real time. Overall, the results illustrate an approach that may help identify therapeutic drugs that temporarily inhibit the leading edge pseudopod during extreme inflammation events, and toxic drugs that yield long term inhibition of the pseudopod with negative consequences for innate immunity. Future studies are needed to elucidate the mechanisms of drug-induced pseudopod collapse, as well as the mechanisms of adaptation and recovery following some inhibitory drug exposures.
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Yoshioka D, Fukushima S, Koteishi H, Okuno D, Ide T, Matsuoka S, Ueda M. Single-molecule imaging of PI(4,5)P 2 and PTEN in vitro reveals a positive feedback mechanism for PTEN membrane binding. Commun Biol 2020; 3:92. [PMID: 32111929 PMCID: PMC7048775 DOI: 10.1038/s42003-020-0818-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/10/2020] [Indexed: 01/21/2023] Open
Abstract
PTEN, a 3-phosphatase of phosphoinositide, regulates asymmetric PI(3,4,5)P3 signaling for the anterior-posterior polarization and migration of motile cells. PTEN acts through posterior localization on the plasma membrane, but the mechanism for this accumulation is poorly understood. Here we developed an in vitro single-molecule imaging assay with various lipid compositions and use it to demonstrate that the enzymatic product, PI(4,5)P2, stabilizes PTEN's membrane-binding. The dissociation kinetics and lateral mobility of PTEN depended on the PI(4,5)P2 density on artificial lipid bilayers. The basic residues of PTEN were responsible for electrostatic interactions with anionic PI(4,5)P2 and thus the PI(4,5)P2-dependent stabilization. Single-molecule imaging in living Dictyostelium cells revealed that these interactions were indispensable for the stabilization in vivo, which enabled efficient cell migration by accumulating PTEN posteriorly to restrict PI(3,4,5)P3 distribution to the anterior. These results suggest that PI(4,5)P2-mediated positive feedback and PTEN-induced PI(4,5)P2 clustering may be important for anterior-posterior polarization.
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Affiliation(s)
- Daisuke Yoshioka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Seiya Fukushima
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hiroyasu Koteishi
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Daichi Okuno
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Toru Ide
- Graduate School of Natural Science and Technology, Okayama University, Okayama-shi, Okayama, 700-8530, Japan
| | - Satomi Matsuoka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan.
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Masahiro Ueda
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan.
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
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14
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Chung JK, Nocka LM, Decker A, Wang Q, Kadlecek TA, Weiss A, Kuriyan J, Groves JT. Switch-like activation of Bruton's tyrosine kinase by membrane-mediated dimerization. Proc Natl Acad Sci U S A 2019; 116:10798-10803. [PMID: 31076553 PMCID: PMC6561188 DOI: 10.1073/pnas.1819309116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The transformation of molecular binding events into cellular decisions is the basis of most biological signal transduction. A fundamental challenge faced by these systems is that reliance on protein-ligand chemical affinities alone generally results in poor sensitivity to ligand concentration, endangering the system to error. Here, we examine the lipid-binding pleckstrin homology and Tec homology (PH-TH) module of Bruton's tyrosine kinase (Btk). Using fluorescence correlation spectroscopy (FCS) and membrane-binding kinetic measurements, we identify a phosphatidylinositol (3-5)-trisphosphate (PIP3) sensing mechanism that achieves switch-like sensitivity to PIP3 levels, surpassing the intrinsic affinity discrimination of PIP3:PH binding. This mechanism employs multiple PIP3 binding as well as dimerization of Btk on the membrane surface. Studies in live cells confirm that mutations at the dimer interface and peripheral site produce effects comparable to that of the kinase-dead Btk in vivo. These results demonstrate how a single protein module can institute an allosteric counting mechanism to achieve high-precision discrimination of ligand concentration. Furthermore, this activation mechanism distinguishes Btk from other Tec family member kinases, Tec and Itk, which we show are not capable of dimerization through their PH-TH modules. This suggests that Btk plays a critical role in the stringency of the B cell response, whereas T cells rely on other mechanisms to achieve stringency.
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Affiliation(s)
- Jean K Chung
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Laura M Nocka
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Aubrianna Decker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Qi Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Theresa A Kadlecek
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
| | - Arthur Weiss
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA 94143
- The Howard Hughes Medical Institute, University of California, San Francisco, CA 94143
| | - John Kuriyan
- Department of Chemistry, University of California, Berkeley, CA 94720;
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA 94720;
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15
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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16
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Yang Y, Shu C, Li P, Igumenova TI. Structural Basis of Protein Kinase Cα Regulation by the C-Terminal Tail. Biophys J 2019; 114:1590-1603. [PMID: 29642029 DOI: 10.1016/j.bpj.2017.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/07/2017] [Accepted: 12/21/2017] [Indexed: 10/17/2022] Open
Abstract
Protein kinase C (PKC) isoenzymes are multi-modular proteins activated at the membrane surface to regulate signal transduction processes. When activated by second messengers, PKC undergoes a drastic conformational and spatial transition from the inactive cytosolic state to the activated membrane-bound state. The complete structure of either state of PKC remains elusive. We demonstrate, using NMR spectroscopy, that the isolated Ca2+-sensing membrane-binding C2 domain of the conventional PKCα interacts with a conserved hydrophobic motif of the kinase C-terminal region, and we report a structural model of the complex. Our data suggest that the C-terminal region plays a dual role in regulating the PKC activity: activating, through sensitization of PKC to intracellular Ca2+ oscillations; and auto-inhibitory, through its interaction with a conserved positively charged region of the C2 domain.
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Affiliation(s)
- Yuan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Chang Shu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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17
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Huang WYC, Alvarez S, Kondo Y, Lee YK, Chung JK, Lam HYM, Biswas KH, Kuriyan J, Groves JT. A molecular assembly phase transition and kinetic proofreading modulate Ras activation by SOS. Science 2019; 363:1098-1103. [PMID: 30846600 PMCID: PMC6563836 DOI: 10.1126/science.aau5721] [Citation(s) in RCA: 208] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/10/2019] [Indexed: 12/15/2022]
Abstract
The guanine nucleotide exchange factor (GEF) Son of Sevenless (SOS) is a key Ras activator that is autoinhibited in the cytosol and activates upon membrane recruitment. Autoinhibition release involves structural rearrangements of the protein at the membrane and thus introduces a delay between initial recruitment and activation. In this study, we designed a single-molecule assay to resolve the time between initial receptor-mediated membrane recruitment and the initiation of GEF activity of individual SOS molecules on microarrays of Ras-functionalized supported membranes. The rise-and-fall shape of the measured SOS activation time distribution and the long mean time scale to activation (~50 seconds) establish a basis for kinetic proofreading in the receptor-mediated activation of Ras. We further demonstrate that this kinetic proofreading is modulated by the LAT (linker for activation of T cells)-Grb2-SOS phosphotyrosine-driven phase transition at the membrane.
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Affiliation(s)
- William Y C Huang
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Steven Alvarez
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
| | - Yasushi Kondo
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Young Kwang Lee
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Jean K Chung
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | | - Kabir H Biswas
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - John Kuriyan
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Divisions of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Divisions of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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18
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A PKC-MARCKS-PI3K regulatory module links Ca2+ and PIP3 signals at the leading edge of polarized macrophages. PLoS One 2018; 13:e0196678. [PMID: 29715315 PMCID: PMC5929533 DOI: 10.1371/journal.pone.0196678] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/17/2018] [Indexed: 12/21/2022] Open
Abstract
The leukocyte chemosensory pathway detects attractant gradients and directs cell migration to sites of inflammation, infection, tissue damage, and carcinogenesis. Previous studies have revealed that local Ca2+ and PIP3 signals at the leading edge of polarized leukocytes play central roles in positive feedback loop essential to cell polarization and chemotaxis. These prior studies showed that stimulation of the leading edge Ca2+ signal can strongly activate PI3K, thereby triggering a larger PIP3 signal, but did not elucidate the mechanistic link between Ca2+ and PIP3 signaling. A hypothesis explaining this link emerged, postulating that Ca2+-activated PKC displaces the MARCKS protein from plasma membrane PIP2, thereby releasing sequestered PIP2 to serve as the target and substrate lipid of PI3K in PIP3 production. In vitro single molecule studies of the reconstituted pathway on lipid bilayers demonstrated the feasibility of this PKC-MARCKS-PI3K regulatory module linking Ca2+ and PIP3 signals in the reconstituted system. The present study tests the model predictions in live macrophages by quantifying the effects of: (a) two pathway activators—PDGF and ATP that stimulate chemoreceptors and Ca2+ influx, respectively; and (b) three pathway inhibitors—wortmannin, EGTA, and Go6976 that inhibit PI3K, Ca2+ influx, and PKC, respectively; on (c) four leading edge activity sensors—AKT-PH-mRFP, CKAR, MARCKSp-mRFP, and leading edge area that report on PIP3 density, PKC activity, MARCKS membrane binding, and leading edge expansion/contraction, respectively. The results provide additional evidence that PKC and PI3K are both essential elements of the leading edge positive feedback loop, and strongly support the existence of a PKC-MARCKS-PI3K regulatory module linking the leading edge Ca2+ and PIP3 signals. As predicted, activators stimulate leading edge PKC activity, displacement of MARCKS from the leading edge membrane and increased leading edge PIP3 levels, while inhibitors trigger the opposite effects. Comparison of the findings for the ameboid chemotaxis of leukocytes with recently published findings for the mesenchymal chemotaxis of fibroblasts suggests that some features of the emerging leukocyte leading edge core pathway (PLC-DAG-Ca2+-PKC-MARCKS-PIP2-PI3K-PIP3) may well be shared by all chemotaxing eukaryotic cells, while other elements of the leukocyte pathway may be specialized features of these highly optimized, professional gradient-seeking cells. More broadly, the findings suggest a molecular mechanism for the strong links between phospho-MARCKS and many human cancers.
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19
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Ven K, Vanspauwen B, Pérez-Ruiz E, Leirs K, Decrop D, Gerstmans H, Spasic D, Lammertyn J. Target Confinement in Small Reaction Volumes Using Microfluidic Technologies: A Smart Approach for Single-Entity Detection and Analysis. ACS Sens 2018; 3:264-284. [PMID: 29363316 DOI: 10.1021/acssensors.7b00873] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the last decades, the study of cells, nucleic acid molecules, and proteins has evolved from ensemble measurements to so-called single-entity studies. The latter offers huge benefits, not only as biological research tools to examine heterogeneities among individual entities within a population, but also as biosensing tools for medical diagnostics, which can reach the ultimate sensitivity by detecting single targets. Whereas various techniques for single-entity detection have been reported, this review focuses on microfluidic systems that physically confine single targets in small reaction volumes. We categorize these techniques as droplet-, microchamber-, and nanostructure-based and provide an overview of their implementation for studying single cells, nucleic acids, and proteins. We furthermore reflect on the advantages and limitations of these techniques and highlight future opportunities in the field.
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Affiliation(s)
- Karen Ven
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Bram Vanspauwen
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Elena Pérez-Ruiz
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Karen Leirs
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Deborah Decrop
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Hans Gerstmans
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Department
of Applied biosciences, Ghent University, Valentyn Vaerwyckweg 1 - building
C, 9000 Gent, Belgium
- Department
of Biosystems, KU Leuven - University of Leuven, Kasteelpark Arenberg
21, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
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20
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Sun L, Gao Y, Xu Y, Chao J, Liu H, Wang L, Li D, Fan C. Real-Time Imaging of Single-Molecule Enzyme Cascade Using a DNA Origami Raft. J Am Chem Soc 2017; 139:17525-17532. [DOI: 10.1021/jacs.7b09323] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Lele Sun
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanjing Gao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Xu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Chao
- Key
Laboratory for Organic Electronics and Information Displays (KLOEID),
Institute of Advanced Materials (IAM), School of Materials Science
and Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210046, China
| | - Huajie Liu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lianhui Wang
- Key
Laboratory for Organic Electronics and Information Displays (KLOEID),
Institute of Advanced Materials (IAM), School of Materials Science
and Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210046, China
| | - Di Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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21
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Morales KA, Yang Y, Cole TR, Igumenova TI. Dynamic Response of the C2 Domain of Protein Kinase Cα to Ca 2+ Binding. Biophys J 2017; 111:1655-1667. [PMID: 27760353 DOI: 10.1016/j.bpj.2016.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/04/2016] [Accepted: 09/07/2016] [Indexed: 11/28/2022] Open
Abstract
Ca2+-dependent conserved-region 2 (C2) domains target their host signaling proteins to anionic membranes. The Ca2+-binding event is a prerequisite for membrane association. Here, we investigate multiscale metal-ion-dependent dynamics of the C2 domain of protein kinase Cα (C2α) using NMR spectroscopy. Interactions with metal ions attenuate microsecond-timescale motions of the loop regions, indicating that preorganization of the metal-binding loops occurs before membrane insertion. Binding of a full complement of Ca2+ ions has a profound effect on the millisecond-timescale dynamics of the N- and C-terminal regions of C2α. We propose that Ca2+ binding allosterically destabilizes the terminal regions of C2α and thereby facilitates the conformational rearrangement necessary for full membrane insertion and activation of protein kinase Cα.
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Affiliation(s)
- Krystal A Morales
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Yuan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Taylor R Cole
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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22
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Regulation of PI3K by PKC and MARCKS: Single-Molecule Analysis of a Reconstituted Signaling Pathway. Biophys J 2017; 110:1811-1825. [PMID: 27119641 DOI: 10.1016/j.bpj.2016.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/09/2016] [Accepted: 03/07/2016] [Indexed: 12/19/2022] Open
Abstract
In chemotaxing ameboid cells, a complex leading-edge signaling circuit forms on the cytoplasmic leaflet of the plasma membrane and directs both actin and membrane remodeling to propel the leading edge up an attractant gradient. This leading-edge circuit includes a putative amplification module in which Ca(2+)-protein kinase C (Ca(2+)-PKC) is hypothesized to phosphorylate myristoylated alanine-rich C kinase substrate (MARCKS) and release phosphatidylinositol-4,5-bisphosphate (PIP2), thereby stimulating production of the signaling lipid phosphatidylinositol-3,4,5-trisphosphate (PIP3) by the lipid kinase phosphoinositide-3-kinase (PI3K). We investigated this hypothesized Ca(2+)-PKC-MARCKS-PIP2-PI3K-PIP3 amplification module and tested its key predictions using single-molecule fluorescence to measure the surface densities and activities of its protein components. Our findings demonstrate that together Ca(2+)-PKC and the PIP2-binding peptide of MARCKS modulate the level of free PIP2, which serves as both a docking target and substrate lipid for PI3K. In the off state of the amplification module, the MARCKS peptide sequesters PIP2 and thereby inhibits PI3K binding to the membrane. In the on state, Ca(2+)-PKC phosphorylation of the MARCKS peptide reverses the PIP2 sequestration, thereby releasing multiple PIP2 molecules that recruit multiple active PI3K molecules to the membrane surface. These findings 1) show that the Ca(2+)-PKC-MARCKS-PIP2-PI3K-PIP3 system functions as an activation module in vitro, 2) reveal the molecular mechanism of activation, 3) are consistent with available in vivo data, and 4) yield additional predictions that are testable in live cells. More broadly, the Ca(2+)-PKC-stimulated release of free PIP2 may well regulate the membrane association of other PIP2-binding proteins, and the findings illustrate the power of single-molecule analysis to elucidate key dynamic and mechanistic features of multiprotein signaling pathways on membrane surfaces.
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23
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Alwarawrah M, Wereszczynski J. Investigation of the Effect of Bilayer Composition on PKCα-C2 Domain Docking Using Molecular Dynamics Simulations. J Phys Chem B 2016; 121:78-88. [PMID: 27997184 DOI: 10.1021/acs.jpcb.6b10188] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The protein kinase Cα (PKCα) enzyme is a member of a broad family of serine/threonine kinases, which are involved in varied cellular signaling pathways. The initial step of PKCα activation involves the C2 subunit docking with the cell membrane, which is followed by interactions of the C1 domains with diacylglycerol (DAG) in the membrane. Notably, the molecular mechanisms of these interactions remain poorly understood, especially what effects, if any, DAG may have on the initial C2 docking. To further understand this process, we have performed a series of conventional molecular dynamics simulations to systematically investigate the interaction between PKCα-C2 domains and lipid bilayers with different compositions to examine the effects of POPS, PIP2, and 1-palmitoyl-2-oleoyl-sn-glycerol (POG) on domain docking. Our results show that the PKCα-C2 domain does not interact with the bilayer surface in the absence of POPS and PIP2. In contrast, the inclusion of POPS and PIP2 to the bilayer resulted in strong domain docking in both perpendicular and parallel orientations, whereas the further inclusion of POG resulted in only parallel domain docking. In addition, lysine residues in the C2 domain formed hydrogen bonds with PIP2 molecule bilayers containing POG. These effects were further explored with umbrella sampling calculations to estimate the free energy of domain docking to the lipid bilayer in the presence of one or two PIP2 molecules. The results show that the binding of one or two PIP2 molecules is thermodynamically favorable, although stronger in bilayers lacking POG. However, in POG-containing bilayers, the binding mode of the C2 domain appears to be more flexible, which may have implications for activation of full-length PKCα. Together, our results shed new insights into the process of C2 bilayer binding and suggest new mechanisms for the roles of different phospholipids in the activation process of PKCα.
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Affiliation(s)
- Mohammad Alwarawrah
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago 60616, Illinois, United States
| | - Jeff Wereszczynski
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago 60616, Illinois, United States
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24
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Ziemba BP, Swisher GH, Masson G, Burke JE, Williams RL, Falke JJ. Regulation of a Coupled MARCKS-PI3K Lipid Kinase Circuit by Calmodulin: Single-Molecule Analysis of a Membrane-Bound Signaling Module. Biochemistry 2016; 55:6395-6405. [PMID: 27933776 DOI: 10.1021/acs.biochem.6b00908] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amoeboid cells that employ chemotaxis to travel up an attractant gradient possess a signaling network assembled on the leading edge of the plasma membrane that senses the gradient and remodels the actin mesh and cell membrane to drive movement in the appropriate direction. In leukocytes such as macrophages and neutrophils, and perhaps in other amoeboid cells as well, the leading edge network includes a positive feedback loop in which the signaling of multiple pathway components is cooperatively coupled. Cytoplasmic Ca2+ is a recently recognized component of the feedback loop at the leading edge where it stimulates phosphoinositide-3-kinase (PI3K) and the production of its product signaling lipid phosphatidylinositol 3,4,5-trisphosphate (PIP3). A previous study implicated Ca2+-activated protein kinase C (PKC) and the phosphatidylinositol 4,5-bisphosphate (PIP2) binding protein MARCKS as two important players in this signaling, because PKC phosphorylation of MARCKS releases free PIP2 that serves as the membrane binding target and substrate for PI3K. This study asks whether calmodulin (CaM), which is known to directly bind MARCKS, also stimulates PIP3 production by releasing free PIP2. Single-molecule fluorescence microscopy is used to quantify the surface density and enzyme activity of key protein components of the hypothesized Ca2+-CaM-MARCKS-PIP2-PI3K-PIP3 circuit. The findings show that CaM does stimulate PI3K lipid kinase activity by binding MARCKS and displacing it from PIP2 headgroups, thereby releasing free PIP2 that recruits active PI3K to the membrane and serves as the substrate for the generation of PIP3. The resulting CaM-triggered activation of PI3K is complete in seconds and is much faster than PKC-triggered activation, which takes minutes. Overall, the available evidence implicates both PKC and CaM in the coupling of Ca2+ and PIP3 signals and suggests these two different pathways have slow and fast activation kinetics, respectively.
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Affiliation(s)
- Brian P Ziemba
- Molecular Biophysics Program and Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - G Hayden Swisher
- Molecular Biophysics Program and Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Glenn Masson
- Laboratory of Molecular Biology, Medical Research Council , Cambridge CB2 0QH, U.K
| | - John E Burke
- Laboratory of Molecular Biology, Medical Research Council , Cambridge CB2 0QH, U.K
| | - Roger L Williams
- Laboratory of Molecular Biology, Medical Research Council , Cambridge CB2 0QH, U.K
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
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Czikora A, Lundberg DJ, Abramovitz A, Lewin NE, Kedei N, Peach ML, Zhou X, Merritt RC, Craft EA, Braun DC, Blumberg PM. Structural Basis for the Failure of the C1 Domain of Ras Guanine Nucleotide Releasing Protein 2 (RasGRP2) to Bind Phorbol Ester with High Affinity. J Biol Chem 2016; 291:11133-47. [PMID: 27022025 PMCID: PMC4900263 DOI: 10.1074/jbc.m116.725333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/28/2016] [Indexed: 11/06/2022] Open
Abstract
The C1 domain represents the recognition module for diacylglycerol and phorbol esters in protein kinase C, Ras guanine nucleotide releasing protein (RasGRP), and related proteins. RasGRP2 is exceptional in that its C1 domain has very weak binding affinity (Kd = 2890 ± 240 nm for [(3)H]phorbol 12,13-dibutyrate. We have identified four amino acid residues responsible for this lack of sensitivity. Replacing Asn(7), Ser(8), Ala(19), and Ile(21) with the corresponding residues from RasGRP1/3 (Thr(7), Tyr(8), Gly(19), and Leu(21), respectively) conferred potent binding affinity (Kd = 1.47 ± 0.03 nm) in vitro and membrane translocation in response to phorbol 12-myristate 13-acetate in LNCaP cells. Mutant C1 domains incorporating one to three of the four residues showed intermediate behavior with S8Y making the greatest contribution. Binding activity for diacylglycerol was restored in parallel. The requirement for anionic phospholipid for [(3)H]phorbol 12,13-dibutyrate binding was determined; it decreased in going from the single S8Y mutant to the quadruple mutant. The full-length RasGRP2 protein with the mutated C1 domains also showed strong phorbol ester binding, albeit modestly weaker than that of the C1 domain alone (Kd = 8.2 ± 1.1 nm for the full-length protein containing all four mutations), and displayed translocation in response to phorbol ester. RasGRP2 is a guanyl exchange factor for Rap1. Consistent with the ability of phorbol ester to induce translocation of the full-length RasGRP2 with the mutated C1 domain, phorbol ester enhanced the ability of the mutated RasGRP2 to activate Rap1. Modeling confirmed that the four mutations helped the binding cleft maintain a stable conformation.
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Affiliation(s)
- Agnes Czikora
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel J Lundberg
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D. C. 20002, and
| | - Adelle Abramovitz
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Nancy E Lewin
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Noemi Kedei
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Megan L Peach
- Basic Science Program, Leidos Biomedical Research, Inc., Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Xiaoling Zhou
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Raymond C Merritt
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D. C. 20002, and
| | - Elizabeth A Craft
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D. C. 20002, and
| | - Derek C Braun
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D. C. 20002, and
| | - Peter M Blumberg
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892,
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26
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Novel Features of DAG-Activated PKC Isozymes Reveal a Conserved 3-D Architecture. J Mol Biol 2016; 428:121-141. [DOI: 10.1016/j.jmb.2015.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/01/2015] [Indexed: 01/17/2023]
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27
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Abstract
Protein kinase C (PKC) is a family of Ser/Thr kinases that regulate a multitude of cellular processes through participation in the phosphoinositide signaling pathway. Significant research efforts have been directed at understanding the structure, function, and regulatory modes of the enzyme since its discovery and identification as the first receptor for tumor-promoting phorbol esters. The activation of PKC involves a transition from the cytosolic autoinhibited latent form to the membrane-associated active form. The membrane recruitment step is accompanied by the conformational rearrangement of the enzyme, which relieves autoinhibitory interactions and thereby allows PKC to phosphorylate its targets. The multidomain structure and intrinsic flexibility of PKC present remarkable challenges and opportunities for the biophysical and structural biology studies of this class of enzymes and their interactions with membranes, the major focus of this Current Topic. I will highlight the recent advances in the field, outline the current challenges, and identify areas where biophysics and structural biology approaches can provide insight into the isoenzyme-specific regulation of PKC activity.
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28
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Harishchandra RK, Neumann BM, Gericke A, Ross AH. Biophysical methods for the characterization of PTEN/lipid bilayer interactions. Methods 2015; 77-78:125-35. [PMID: 25697761 PMCID: PMC4388815 DOI: 10.1016/j.ymeth.2015.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 12/22/2022] Open
Abstract
PTEN, a tumor suppressor protein that dephosphorylates phosphoinositides at the 3-position of the inositol ring, is a cytosolic protein that needs to associate with the plasma membrane or other subcellular membranes to exert its lipid phosphatase function. Upon membrane association PTEN interacts with at least three different lipid entities: An anionic lipid that is present in sufficiently high concentration to create a negative potential that allows PTEN to interact electrostatically with the membrane, phosphatidylinositol-4,5-bisphosphate, which interacts with PTEN's N-terminal end and the substrate, usually phosphatidylinositol-3,4,5-trisphosphate. Many parameters influence PTEN's interaction with the lipid bilayer, for example, the lateral organization of the lipids or the presence of other chemical species like cholesterol or other lipids. To investigate systematically the different steps of PTEN's complex binding mechanism and to explore its dynamic behavior in the membrane bound state, in vitro methods need to be employed that allow for a systematic variation of the experimental conditions. In this review we survey a variety of methods that can be used to assess PTEN lipid binding affinity, the dynamics of its membrane association as well as its dynamic behavior in the membrane bound state.
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Affiliation(s)
- Rakesh K Harishchandra
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, Worcester, MA 01605, USA
| | - Brittany M Neumann
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, Worcester, MA 01605, USA
| | - Arne Gericke
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, Worcester, MA 01605, USA
| | - Alonzo H Ross
- University of Massachusetts Medical School, Department of Biochemistry and Molecular Pharmacology, Worcester, MA 01605, USA.
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29
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Lee IH, Saha S, Polley A, Huang H, Mayor S, Rao M, Groves JT. Live cell plasma membranes do not exhibit a miscibility phase transition over a wide range of temperatures. J Phys Chem B 2015; 119:4450-9. [PMID: 25747462 DOI: 10.1021/jp512839q] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Lipid/cholesterol mixtures derived from cell membranes as well as their synthetic reconstitutions exhibit well-defined miscibility phase transitions and critical phenomena near physiological temperatures. This suggests that lipid/cholesterol-mediated phase separation plays a role in the organization of live cell membranes. However, macroscopic lipid-phase separation is not generally observed in cell membranes, and the degree to which properties of isolated lipid mixtures are preserved in the cell membrane remain unknown. A fundamental property of phase transitions is that the variation of tagged particle diffusion with temperature exhibits an abrupt change as the system passes through the transition, even when the two phases are distributed in a nanometer-scale emulsion. We support this using a variety of Monte Carlo and atomistic simulations on model lipid membrane systems. However, temperature-dependent fluorescence correlation spectroscopy of labeled lipids and membrane-anchored proteins in live cell membranes shows a consistently smooth increase in the diffusion coefficient as a function of temperature. We find no evidence of a discrete miscibility phase transition throughout a wide range of temperatures: 14-37 °C. This contrasts the behavior of giant plasma membrane vesicles (GPMVs) blebbed from the same cells, which do exhibit phase transitions and macroscopic phase separation. Fluorescence lifetime analysis of a DiI probe in both cases reveals a significant environmental difference between the live cell and the GPMV. Taken together, these data suggest the live cell membrane may avoid the miscibility phase transition inherent to its lipid constituents by actively regulating physical parameters, such as tension, in the membrane.
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Affiliation(s)
- Il-Hyung Lee
- †Department of Chemistry, California Institute for Quantitative Biosciences (QB3), Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States
| | - Suvrajit Saha
- §National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore 560065, India
| | - Anirban Polley
- ∥Raman Research Institute, C.V. Raman Avenue, Bangalore 560080, India
| | - Hector Huang
- †Department of Chemistry, California Institute for Quantitative Biosciences (QB3), Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States
| | - Satyajit Mayor
- §National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore 560065, India
| | - Madan Rao
- §National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore 560065, India.,∥Raman Research Institute, C.V. Raman Avenue, Bangalore 560080, India
| | - Jay T Groves
- †Department of Chemistry, California Institute for Quantitative Biosciences (QB3), Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States.,‡Materials Sciences Division, Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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30
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Loy BA, Lesser AB, Staveness D, Billingsley KL, Cegelski L, Wender PA. Toward a biorelevant structure of protein kinase C bound modulators: design, synthesis, and evaluation of labeled bryostatin analogues for analysis with rotational echo double resonance NMR spectroscopy. J Am Chem Soc 2015; 137:3678-85. [PMID: 25710634 DOI: 10.1021/jacs.5b00886] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein kinase C (PKC) modulators are currently of great importance in preclinical and clinical studies directed at cancer, immunotherapy, HIV eradication, and Alzheimer's disease. However, the bound conformation of PKC modulators in a membrane environment is not known. Rotational echo double resonance (REDOR) NMR spectroscopy could uniquely address this challenge. However, REDOR NMR requires strategically labeled, high affinity ligands to determine interlabel distances from which the conformation of the bound ligand in the PKC-ligand complex could be identified. Here we report the first computer-guided design and syntheses of three bryostatin analogues strategically labeled for REDOR NMR analysis. Extensive computer analyses of energetically accessible analogue conformations suggested preferred labeling sites for the identification of the PKC-bound conformers. Significantly, three labeled analogues were synthesized, and, as required for REDOR analysis, all proved highly potent with PKC affinities (∼1 nM) on par with bryostatin. These potent and strategically labeled bryostatin analogues are new structural leads and provide the necessary starting point for projected efforts to determine the PKC-bound conformation of such analogues in a membrane environment, as needed to design new PKC modulators and understand PKC-ligand-membrane structure and dynamics.
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Affiliation(s)
- Brian A Loy
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Adam B Lesser
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Daryl Staveness
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Kelvin L Billingsley
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Lynette Cegelski
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Paul A Wender
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
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31
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Cole TR, Igumenova TI. Expression and purification of the N-terminal regulatory domain of Protein Kinase C for biophysical studies. Protein Expr Purif 2015; 110:14-21. [PMID: 25582765 DOI: 10.1016/j.pep.2014.12.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/20/2014] [Accepted: 12/25/2014] [Indexed: 11/25/2022]
Abstract
We report the protocol for heterologous expression and purification of the N-terminal regulatory region of two Protein Kinase C (PKC)(1) isozymes, one conventional and one novel. Previous studies of these domains relied almost exclusively on the fusion constructs with high-molecular-weight solubility fusion partners such as GST and MBP. We developed experimental procedures that enabled us to overcome challenges associated with the amphiphilic character of the regulatory domain and generate sufficient quantities of fusion partner-free proteins for biophysical work. The key features of the protocol are the identity of the cleavable fusion partner, expression conditions, growth medium additives, introduction of mutation/solubility tags, and incorporation of osmolytes. The protein yields are sufficient for cost-effective production of isotopically enriched proteins for NMR work and biophysical studies in general. Our work opens up an avenue for the structural studies of these challenging proteins with high amphiphilic character.
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Affiliation(s)
- Taylor R Cole
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843, USA
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843, USA.
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32
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Colomb W, Sarkar SK. Extracting physics of life at the molecular level: A review of single-molecule data analyses. Phys Life Rev 2015; 13:107-37. [PMID: 25660417 DOI: 10.1016/j.plrev.2015.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 12/31/2022]
Abstract
Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.
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Affiliation(s)
- Warren Colomb
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States
| | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States.
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33
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Lucke-Wold BP, Turner RC, Logsdon AF, Simpkins JW, Alkon DL, Smith KE, Chen YW, Tan Z, Huber JD, Rosen CL. Common mechanisms of Alzheimer's disease and ischemic stroke: the role of protein kinase C in the progression of age-related neurodegeneration. J Alzheimers Dis 2015; 43:711-24. [PMID: 25114088 PMCID: PMC4446718 DOI: 10.3233/jad-141422] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ischemic stroke and Alzheimer's disease (AD), despite being distinct disease entities, share numerous pathophysiological mechanisms such as those mediated by inflammation, immune exhaustion, and neurovascular unit compromise. An important shared mechanistic link is acute and chronic changes in protein kinase C (PKC) activity. PKC isoforms have widespread functions important for memory, blood-brain barrier maintenance, and injury repair that change as the body ages. Disease states accelerate PKC functional modifications. Mutated forms of PKC can contribute to neurodegeneration and cognitive decline. In some cases the PKC isoforms are still functional but are not successfully translocated to appropriate locations within the cell. The deficits in proper PKC translocation worsen stroke outcome and amyloid-β toxicity. Cross talk between the innate immune system and PKC pathways contribute to the vascular status within the aging brain. Unfortunately, comorbidities such as diabetes, obesity, and hypertension disrupt normal communication between the two systems. The focus of this review is to highlight what is known about PKC function, how isoforms of PKC change with age, and what additional alterations are consequences of stroke and AD. The goal is to highlight future therapeutic targets that can be applied to both the treatment and prevention of neurologic disease. Although the pathology of ischemic stroke and AD are different, the similarity in PKC responses warrants further investigation, especially as PKC-dependent events may serve as an important connection linking age-related brain injury.
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Affiliation(s)
- Brandon P. Lucke-Wold
- Department of Neurosurgery, West Virginia University School of Medicine, Morgantown, WV, USA
- The Center for Neuroscience, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Ryan C. Turner
- Department of Neurosurgery, West Virginia University School of Medicine, Morgantown, WV, USA
- The Center for Neuroscience, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Aric F. Logsdon
- The Center for Neuroscience, West Virginia University School of Medicine, Morgantown, WV, USA
- Department of Basic Pharmaceutical Sciences, West Virginia University School of Pharmacy, Morgantown, WV, USA
| | - James W. Simpkins
- The Center for Neuroscience, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Daniel L. Alkon
- Blanchette Rockefeller Neurosciences Institute, Morgantown, WV, USA
| | - Kelly E. Smith
- The Center for Neuroscience, West Virginia University School of Medicine, Morgantown, WV, USA
- Department of Basic Pharmaceutical Sciences, West Virginia University School of Pharmacy, Morgantown, WV, USA
| | - Yi-Wen Chen
- The Center for Neuroscience, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Zhenjun Tan
- Department of Neurosurgery, West Virginia University School of Medicine, Morgantown, WV, USA
- The Center for Neuroscience, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Jason D. Huber
- The Center for Neuroscience, West Virginia University School of Medicine, Morgantown, WV, USA
- Department of Basic Pharmaceutical Sciences, West Virginia University School of Pharmacy, Morgantown, WV, USA
| | - Charles L. Rosen
- Department of Neurosurgery, West Virginia University School of Medicine, Morgantown, WV, USA
- The Center for Neuroscience, West Virginia University School of Medicine, Morgantown, WV, USA
- Correspondence to: Charles L. Rosen, MD, PhD, Department of Neurosurgery, West Virginia University School of Medicine, One Medical Center Drive, Suite 4300, Health Sciences Center, PO Box 9183, Morgantown, WV 26506-9183, USA. Tel.: +1 304 293 5041; Fax: +1 304 293 4819;
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34
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Vasquez JK, Chantranuvatana K, Giardina DT, Coffman MD, Knight JD. Lateral diffusion of proteins on supported lipid bilayers: additive friction of synaptotagmin 7 C2A-C2B tandem domains. Biochemistry 2014; 53:7904-13. [PMID: 25437758 PMCID: PMC4278679 DOI: 10.1021/bi5012223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
The
synaptotagmin (Syt) family of proteins contains tandem C2 domains,
C2A and C2B, which bind membranes in the presence of Ca2+ to trigger vesicle fusion during exocytosis. Despite recent progress,
the role and extent of interdomain interactions between C2A and C2B
in membrane binding remain unclear. To test whether the two domains
interact on a planar lipid bilayer (i.e., experience thermodynamic
interdomain contacts), diffusion of fluorescent-tagged C2A, C2B, and
C2AB domains from human Syt7 was measured using total internal reflection
fluorescence microscopy with single-particle tracking. The C2AB tandem
exhibits a lateral diffusion constant approximately half the value
of the isolated single domains and does not change when additional
residues are engineered into the C2A–C2B linker. This is the
expected result if C2A and C2B are separated when membrane-bound;
theory predicts that C2AB diffusion would be faster if the two domains
were close enough together to have interdomain contact. Stopped-flow
measurements of membrane dissociation kinetics further support an
absence of interdomain interactions, as dissociation kinetics of the
C2AB tandem remain unchanged when rigid or flexible linker extensions
are included. Together, the results suggest that the two C2 domains
of Syt7 bind independently to planar membranes, in contrast to reported
interdomain cooperativity in Syt1.
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Affiliation(s)
- Joseph K Vasquez
- Department of Chemistry, University of Colorado Denver , Denver, Colorado 80217, United States
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35
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Wender PA, Nakagawa Y, Near KE, Staveness D. Computer-guided design, synthesis, and protein kinase C affinity of a new salicylate-based class of bryostatin analogs. Org Lett 2014; 16:5136-9. [PMID: 25238583 PMCID: PMC4334246 DOI: 10.1021/ol502491f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Bryostatin 1 is in
clinical trials for the treatment of cancer
and Alzheimer’s disease and is a candidate for a first-in-class
approach to HIV/AIDS eradication. It is neither readily available
nor optimally suited for clinical use. Using a function oriented synthesis
strategy, a new class of bryostatin-inspired analogs was designed
with a simplified salicylate-derived subunit, enabling step-economical
synthesis (23 total steps) of agents exhibiting bryostatin-like affinity
to protein kinase C (PKC).
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Affiliation(s)
- Paul A Wender
- Departments of Chemistry and Chemical and Systems Biology, Stanford University , Stanford, California 94305, United States
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36
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Li J, Ziemba BP, Falke J, Voth GA. Interactions of protein kinase C-α C1A and C1B domains with membranes: a combined computational and experimental study. J Am Chem Soc 2014; 136:11757-66. [PMID: 25075641 PMCID: PMC4140453 DOI: 10.1021/ja505369r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Indexed: 02/01/2023]
Abstract
Protein kinase C-α (PKCα) has been studied widely as a paradigm for conventional PKCs, with two C1 domains (C1A and C1B) being important for the regulation and function of the kinase. However, it is challenging to explore these domains in membrane-bound environments with either simulations or experiments alone. In this work, we have combined modeling, simulations, and experiments to understand the molecular basis of the PKCα C1A and C1B domain interactions with membranes. Our atomistic simulations of the PKCα C1 domains reveal the dynamic interactions of the proteins with anionic lipids, as well as the conserved hydrogen bonds and the distinct nonpolar contacts formed with lipid activators. Corroborating evidence is obtained from additional simulations and experiments in terms of lipid binding and protein diffusion. Overall, our study, for the first time, explains with atomistic detail how the PKCα C1A and C1B domains interact differently with various lipids. On the molecular level, the information provided by our study helps to shed light on PKCα regulation and activation mechanism. The combined computational/experimental approach demonstrated in this work is anticipated to enable further studies to explore the roles of C1 domains in many signaling proteins and to better understand their molecular mechanisms in normal cellular function and disease development.
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Affiliation(s)
- Jianing Li
- Department
of Chemistry, Institute for Biophysical Dynamics, James Franck Institute
and Computation Institute, The University
of Chicago, 5735 South
Ellis Avenue, Chicago, Illinois 60637, United States
| | - Brian P. Ziemba
- Department
of Chemistry and Biochemistry and the Molecular Biophysics Program, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Joseph
J. Falke
- Department
of Chemistry and Biochemistry and the Molecular Biophysics Program, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Gregory A. Voth
- Department
of Chemistry, Institute for Biophysical Dynamics, James Franck Institute
and Computation Institute, The University
of Chicago, 5735 South
Ellis Avenue, Chicago, Illinois 60637, United States
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37
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Stewart MD, Cole TR, Igumenova TI. Interfacial partitioning of a loop hinge residue contributes to diacylglycerol affinity of conserved region 1 domains. J Biol Chem 2014; 289:27653-64. [PMID: 25124034 DOI: 10.1074/jbc.m114.585570] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Conventional and novel isoenzymes of PKC are activated by the membrane-embedded second messenger diacylglycerol (DAG) through its interactions with the C1 regulatory domain. The affinity of C1 domains to DAG varies considerably among PKCs. To gain insight into the origin of differential DAG affinities, we conducted high-resolution NMR studies of C1B domain from PKCδ (C1Bδ) and its W252Y variant. The W252Y mutation was previously shown to render C1Bδ less responsive to DAG (Dries, D. R., Gallegos, L. L., and Newton, A. C. (2007) A single residue in the C1 domain sensitizes novel protein kinase C isoforms to cellular diacylglycerol production. J. Biol. Chem. 282, 826-830) and thereby emulate the behavior of C1B domains from conventional PKCs that have a conserved Tyr at the equivalent position. Our data revealed that W252Y mutation did not perturb the conformation of C1Bδ in solution but significantly reduced its propensity to partition into a membrane-mimicking environment in the absence of DAG. Using detergent micelles doped with a paramagnetic lipid, we determined that both the residue identity at position 252 and complexation with diacylglycerol influence the geometry of C1Bδ-micelle interactions. In addition, we identified the C-terminal helix α1 of C1Bδ as an interaction site with the head groups of phosphatidylserine, a known activator of PKCδ. Taken together, our studies (i) reveal the identities of C1Bδ residues involved in interactions with membrane-mimicking environment, DAG, and phosphatidylserine, as well as the affinities associated with each event and (ii) suggest that the initial ligand-independent membrane recruitment of C1B domains, which is greatly facilitated by the interfacial partitioning of Trp-252, is responsible, at least in part, for the differential DAG affinities.
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Affiliation(s)
- Mikaela D Stewart
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Taylor R Cole
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Tatyana I Igumenova
- From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
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38
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Swanson CJ, Ritt M, Wang W, Lang MJ, Narayan A, Tesmer JJ, Westfall M, Sivaramakrishnan S. Conserved modular domains team up to latch-open active protein kinase Cα. J Biol Chem 2014; 289:17812-29. [PMID: 24790081 DOI: 10.1074/jbc.m113.534750] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Signaling proteins comprised of modular domains have evolved along with multicellularity as a method to facilitate increasing intracellular bandwidth. The effects of intramolecular interactions between modular domains within the context of native proteins have been largely unexplored. Here we examine intra- and intermolecular interactions in the multidomain signaling protein, protein kinase Cα (PKCα). We identify three interactions between two activated PKC molecules that synergistically stabilize a nanomolar affinity homodimer. Disruption of the homodimer results in a loss of PKC-mediated ERK1/2 phosphorylation, whereas disruption of the auto-inhibited state promotes the homodimer and prolongs PKC membrane localization. These observations support a novel regulatory mechanism wherein homodimerization dictates the equilibrium between the auto-inhibited and active states of PKC by sequestering auto-inhibitory interactions. Our findings underscore the physiological importance of context-dependent modular domain interactions in cell signaling.
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Affiliation(s)
| | | | - William Wang
- Department of Cell and Developmental Biology, Department of Cardiac Surgery
| | | | - Arvind Narayan
- Department of Biomedical Engineering, Life Sciences Institute, and
| | - John J Tesmer
- From the Biophysics Program, the Departments of Pharmacology and Biological Sciences, University of Michigan, Ann Arbor, Michigan 48109
| | - Margaret Westfall
- Department of Cardiac Surgery, Department of Biomedical Engineering, Life Sciences Institute, and
| | - Sivaraj Sivaramakrishnan
- From the Biophysics Program, Department of Cell and Developmental Biology, Department of Biomedical Engineering, Life Sciences Institute, and
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