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Zhou Y, Roseli RB, Hungerford NL, Fletcher MT, Ouwerkerk D, Gilbert RA, Krenske EH. Binding of the plant-derived toxin simplexin to bovine protein kinase C: insights from molecular dynamics. Org Biomol Chem 2024; 22:2863-2876. [PMID: 38525790 DOI: 10.1039/d4ob00065j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Pimelea poisoning of cattle is toxicologically linked to the activation of bovine protein kinase C (PKC) by the plant-derived toxin simplexin. To understand the affinity of PKC for simplexin, we performed molecular dynamics (MD) studies of simplexin, simplexin analogues, and several other activators of PKC. Binding enthalpy calculations indicated that simplexin had the strongest affinity for PKCα-C1B among the activators studied. Key to simplexin's affinity is its ability to form more hydrogen bonds to PKC, compared to the other activators. The C-3 carbonyl group and C-20 hydroxyl group of simplexin were identified as especially important for stabilizing the PKC binding interaction. The hydrophobic alkyl chain of simplexin induces deep membrane embedding of the PKC-simplexin complex, enhancing the protein-ligand hydrogen bonding. Our findings align with previous experiments on structure-activity relationships (SAR) for simplexin analogues, and provide insights that may guide the development of interventions or treatments for Pimelea poisoning.
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Affiliation(s)
- Yuchen Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
| | - Ras Baizureen Roseli
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
| | - Natasha L Hungerford
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Health and Food Sciences Precinct, Coopers Plains, QLD 4108, Australia
| | - Mary T Fletcher
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Health and Food Sciences Precinct, Coopers Plains, QLD 4108, Australia
| | - Diane Ouwerkerk
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), EcoSciences Precinct, Dutton Park, Queensland, 4102, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Queensland Bioscience Precinct, St Lucia, QLD 4072, Australia
| | - Rosalind A Gilbert
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), EcoSciences Precinct, Dutton Park, Queensland, 4102, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Queensland Bioscience Precinct, St Lucia, QLD 4072, Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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2
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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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3
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Insertion Depth Modulates Protein Kinase C-δ-C1b Domain Interactions with Membrane Cholesterol as Revealed by MD Simulations. Int J Mol Sci 2023; 24:ijms24054598. [PMID: 36902029 PMCID: PMC10002858 DOI: 10.3390/ijms24054598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Protein kinase C delta (PKC-δ) is an important signaling molecule in human cells that has both proapoptotic as well as antiapoptotic functions. These conflicting activities can be modulated by two classes of ligands, phorbol esters and bryostatins. Phorbol esters are known tumor promoters, while bryostatins have anti-cancer properties. This is despite both ligands binding to the C1b domain of PKC-δ (δC1b) with a similar affinity. The molecular mechanism behind this discrepancy in cellular effects remains unknown. Here, we have used molecular dynamics simulations to investigate the structure and intermolecular interactions of these ligands bound to δC1b with heterogeneous membranes. We observed clear interactions between the δC1b-phorbol complex and membrane cholesterol, primarily through the backbone amide of L250 and through the K256 side-chain amine. In contrast, the δC1b-bryostatin complex did not exhibit interactions with cholesterol. Topological maps of the membrane insertion depth of the δC1b-ligand complexes suggest that insertion depth can modulate δC1b interactions with cholesterol. The lack of cholesterol interactions suggests that bryostatin-bound δC1b may not readily translocate to cholesterol-rich domains within the plasma membrane, which could significantly alter the substrate specificity of PKC-δ compared to δC1b-phorbol complexes.
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4
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Heinonen S, Lautala S, Koivuniemi A, Bunker A. Insights into the behavior of unsaturated diacylglycerols in mixed lipid bilayers in relation to protein kinase C activation-A molecular dynamics simulation study. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183961. [PMID: 35568204 DOI: 10.1016/j.bbamem.2022.183961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The lipid second messenger diacylglycerol (DAG) is known for its involvement in many types of cellular signaling, especially as an endogenous agonist for protein kinase C (PKC). Evidence has emerged that the degree of saturation of the DAG molecules can affect PKC activation. DAG molecules with different acyl chain saturation have not only been observed to induce varying extents of PKC activation, but also to express selectivity towards different PKC isozymes. Both qualities are important for precise therapeutic activation of PKC; understanding DAG behavior at the molecular level in different environments has much potential in the development of drugs to target PKC. We used molecular dynamics simulations to study the behavior of two different unsaturated DAG species in lipid environments with varying degrees of unsaturation. We focus on phosphatidylethanolamine (PE) instead of phosphatidylcholine (PC) to more accurately model the relevant biomembranes. The effect of cholesterol (CHOL) on these systems was also explored. We found that both high level of unsaturation in the acyl chains of the DAG species and presence of CHOL in the surrounding membrane increase DAG molecule availability at the lipid-water interface. This can partially explain the previously observed differences in PKC activation strength and specificity, the complete mechanism is, however, likely to be more complex. Our simulations coupled with the current understanding of lipids highlight the need for more simulations of biologically accurate lipid environments in order to determine the correct correlations between molecular mechanisms and biological behavior when studying PKC activation.
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Affiliation(s)
- Suvi Heinonen
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Saara Lautala
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, FI-00014, Helsinki, Finland.
| | - Artturi Koivuniemi
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
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5
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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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6
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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: 13] [Impact Index Per Article: 6.5] [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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7
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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8
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Katti S, Igumenova TI. Structural insights into C1-ligand interactions: Filling the gaps by in silico methods. Adv Biol Regul 2021; 79:100784. [PMID: 33526356 DOI: 10.1016/j.jbior.2020.100784] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023]
Abstract
Protein Kinase C isoenzymes (PKCs) are the key mediators of the phosphoinositide signaling pathway, which involves regulated hydrolysis of phosphatidylinositol (4,5)-bisphosphate to diacylglycerol (DAG) and inositol-1,4,5-trisphosphate. Dysregulation of PKCs is implicated in many human diseases making this class of enzymes an important therapeutic target. Specifically, the DAG-sensing cysteine-rich conserved homology-1 (C1) domains of PKCs have emerged as promising targets for pharmaceutical modulation. Despite significant progress, the rational design of the C1 modulators remains challenging due to difficulties associated with structure determination of the C1-ligand complexes. Given the dearth of experimental structural data, computationally derived models have been instrumental in providing atomistic insight into the interactions of the C1 domains with PKC agonists. In this review, we provide an overview of the in silico approaches for seven classes of C1 modulators and outline promising future directions.
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Affiliation(s)
- Sachin Katti
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, United States
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, United States.
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9
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Lautala S, Provenzani R, Koivuniemi A, Kulig W, Talman V, Róg T, Tuominen RK, Yli-Kauhaluoma J, Bunker A. Rigorous Computational Study Reveals What Docking Overlooks: Double Trouble from Membrane Association in Protein Kinase C Modulators. J Chem Inf Model 2020; 60:5624-5633. [PMID: 32915560 DOI: 10.1021/acs.jcim.0c00624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Increasing protein kinase C (PKC) activity is of potential therapeutic value. Its activation involves an interaction between the C1 domain and diacylglycerol (DAG) at intracellular membrane surfaces; DAG mimetics hold promise as new drugs. We previously developed the isophthalate derivative HMI-1a3, an effective but highly lipophilic (clogP = 6.46) DAG mimetic. Although a less lipophilic pyrimidine analog, PYR-1gP (clogP = 3.30), gave positive results in computational docking, it unexpectedly presented greatly diminished binding to PKC in vitro. Through more rigorous computational molecular modeling, we reveal that, unlike HMI-1a3, PYR-1gP forms an intramolecular hydrogen bond, which both obstructs binding and reorients PYR-1gP in the membrane in a fashion that prevents it from correctly accessing the PKC C1 domain. Our results highlight the great value of molecular dynamics simulations as a key component for the drug design process of ligands targeting weakly membrane-associated proteins, where simulation in the relevant membrane environment is crucial for obtaining biologically applicable results.
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Affiliation(s)
- Saara Lautala
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
| | - Riccardo Provenzani
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
| | - Artturi Koivuniemi
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, P.O. Box 64, Gustaf Hällströmin katu 2, FI-00014 Helsinki, Finland
| | - Virpi Talman
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland.,National Heart and Lung Institute, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom
| | - Tomasz Róg
- Department of Physics, University of Helsinki, P.O. Box 64, Gustaf Hällströmin katu 2, FI-00014 Helsinki, Finland
| | - Raimo K Tuominen
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 Helsinki, Finland
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10
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Travers T, López CA, Agamasu C, Hettige JJ, Messing S, García AE, Stephen AG, Gnanakaran S. Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD. Biophys J 2020; 119:525-538. [PMID: 32649863 PMCID: PMC7399501 DOI: 10.1016/j.bpj.2020.06.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/12/2020] [Accepted: 06/18/2020] [Indexed: 11/25/2022] Open
Abstract
CRAF activation requires binding to membrane-anchored and active GTP-bound RAS. Whereas its RAS-binding domain (RBD) contains the main binding interface to the RAS G domain, its cysteine-rich domain (CRD) is responsible for association to anionic lipid-rich membranes. Both RAF domains are connected by a short linker, and it remains unclear if the two domains act independently or if one domain can impact the function of the other. Here, we used a combination of coarse-grained and all-atom molecular dynamics simulations of a CRAF RBD-CRD construct to investigate the dynamics of the RBD when it is tethered to CRD that is anchored to a POPC:POPS model membrane. First, we show that the RBD positioning is very dynamic with a preferential localization near the membrane surface. Next, we show that membrane-localized RBD has its RAS-binding interface mostly inaccessible because of its proximity to the membrane. Several positively charged residues in this interface were identified from simulations as important for driving RBD association to the membrane. Surface plasmon resonance (SPR) measurements confirmed that mutations of these RBD residues reduced the liposome partitioning of RBD-CRD. Last, simulations indicated that the presence of RBD near the membrane led to a local enrichment of anionic lipids that could potentially enhance the membrane affinity of the entire RBD-CRD construct. This was supported by SPR measurements that showed stronger liposome partitioning of RBD-CRD relative to CRD alone. These findings thus suggest that the RBD and CRD have synergistic effects on their membrane dynamics, with CRD bringing RBD closer to the membrane that impacts its accessibility to RAS and with RBD causing local anionic lipid enrichment that enhances the overall affinity between the membrane and RBD-CRD. These mechanisms have potential implications on the order of events of the interactions between RAS and CRAF at the membrane.
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Affiliation(s)
- Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico
| | - Constance Agamasu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | | | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | - Angel E García
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico.
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11
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Pak Dek MS, Padmanabhan P, Tiwari K, Todd JF, Paliyath G. Structural and functional characterization of Solanum lycopersicum phosphatidylinositol 3-kinase C2 domain. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:180-192. [PMID: 31972387 DOI: 10.1016/j.plaphy.2020.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/10/2020] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
Phosphatidylinositol 3-kinases (PI3Ks) are characterized by the presence of a C2 domain at the N-terminal end (class I, III); or at both the N-terminal and C-terminal ends (class II), sometimes including a Plextrin homology domain and/or a Ras domain. Plant PI3Ks are analogous to the class III mammalian PI3K. An N-terminal fragment (~170 aa) of the tomato PI3K regulatory domain including the C2 domain, was cloned and expressed in a bacterial system. This protein was purified to homogeneity and its physicochemical properties analyzed. The purified protein showed strong binding with monophosphorylated phosphatidylinositols, and the binding was dependent on calcium ion concentration and pH. In the overall tertiary structure of PI3K, C2 domain showed unique characteristics, having three antiparallel beta-sheets, hydrophobic regions, acidic as well as alkaline motifs, that can enable its membrane binding upon activation. To elucidate the functional significance of C2 domain, transgenic tobacco plants expressing the C2 domain of PI3K were generated. Transgenic plants showed defective pollen development and disrupted seed set. Flowers from the PI3K-C2 transgenic plants showed delayed wilting, and a decrease in ethylene production. It is likely that introduction of the PI3K-C2 segment may have interfered with the normal binding of PI3K to the membrane, delaying the onset of membrane lipid catabolism that lead to senescence.
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Affiliation(s)
- Mohd Sabri Pak Dek
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Priya Padmanabhan
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Krishnaraj Tiwari
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - James F Todd
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Ontario Ministry of Agriculture, Food and Rural Affairs, Simcoe Research Station, Ontario, Canada
| | - Gopinadhan Paliyath
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
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12
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Reinhardt R, Truebestein L, Schmidt HA, Leonard TA. It Takes Two to Tango: Activation of Protein Kinase D by Dimerization. Bioessays 2020; 42:e1900222. [PMID: 31997382 DOI: 10.1002/bies.201900222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/10/2020] [Indexed: 12/23/2022]
Abstract
The recent discovery and structure determination of a novel ubiquitin-like dimerization domain in protein kinase D (PKD) has significant implications for its activation. PKD is a serine/threonine kinase activated by the lipid second messenger diacylglycerol (DAG). It is an essential and highly conserved protein that is implicated in plasma membrane directed trafficking processes from the trans-Golgi network. However, many open questions surround its mechanism of activation, its localization, and its role in the biogenesis of cargo transport carriers. In reviewing this field, the focus is primarily on the mechanisms that control the activation of PKD at precise locations in the cell. In light of the new structural findings, the understanding of the mechanisms underlying PKD activation is critically evaluated, with particular emphasis on the role of dimerization in PKD autophosphorylation, and the provenance and recognition of the DAG that activates PKD.
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Affiliation(s)
- Ronja Reinhardt
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter, 1030, Vienna, Austria.,Department of Medical Biochemistry, Medical University of Vienna, 1030, Vienna, Austria
| | - Linda Truebestein
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter, 1030, Vienna, Austria.,Department of Medical Biochemistry, Medical University of Vienna, 1030, Vienna, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna Biocenter, 1030, Vienna, Austria
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter, 1030, Vienna, Austria.,Department of Medical Biochemistry, Medical University of Vienna, 1030, Vienna, Austria
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13
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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: 173] [Impact Index Per Article: 34.6] [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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14
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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15
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Travers T, López CA, Van QN, Neale C, Tonelli M, Stephen AG, Gnanakaran S. Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain. Sci Rep 2018; 8:8461. [PMID: 29855542 PMCID: PMC5981303 DOI: 10.1038/s41598-018-26832-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/18/2018] [Indexed: 01/14/2023] Open
Abstract
Activation of RAF kinase involves the association of its RAS-binding domain (RBD) and cysteine-rich domain (CRD) with membrane-anchored RAS. However, the overall architecture of the RAS/RBD/CRD ternary complex and the orientations of its constituent domains at the membrane remain unclear. Here, we have combined all-atom and coarse-grained molecular dynamics (MD) simulations with experimental data to construct and validate a model of membrane-anchored CRD, and used this as a basis to explore models of membrane-anchored RAS/RBD/CRD complex. First, simulations of the CRD revealed that it anchors to the membrane via insertion of its two hydrophobic loops, which is consistent with our NMR measurements of CRD bound to nanodiscs. Simulations of the CRD in the context of membrane-anchored RAS/RBD then show how CRD association with either RAS or RBD could play an unexpected role in guiding the membrane orientations of RAS/RBD. This finding has implications for the formation of RAS-RAS dimers, as different membrane orientations of RAS expose distinct putative dimerization interfaces.
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Affiliation(s)
- Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Que N Van
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 21702, United States
| | - Chris Neale
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Marco Tonelli
- National Magnetic Resource Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 21702, United States
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States.
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16
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Yang H, Staveness D, Ryckbosch SM, Axtman AD, Loy BA, Barnes AB, Pande VS, Schaefer J, Wender PA, Cegelski L. REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment. ACS CENTRAL SCIENCE 2018; 4:89-96. [PMID: 29392180 PMCID: PMC5785774 DOI: 10.1021/acscentsci.7b00475] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Indexed: 05/05/2023]
Abstract
Bryostatin 1 (henceforth bryostatin) is in clinical trials for the treatment of Alzheimer's disease and for HIV/AIDS eradication. It is also a preclinical lead for cancer immunotherapy and other therapeutic indications. Yet nothing is known about the conformation of bryostatin bound to its protein kinase C (PKC) target in a membrane microenvironment. As a result, efforts to design more efficacious, better tolerated, or more synthetically accessible ligands have been limited to structures that do not include PKC or membrane effects known to influence PKC-ligand binding. This problem extends more generally to many membrane-associated proteins in the human proteome. Here, we use rotational-echo double-resonance (REDOR) solid-state NMR to determine the conformations of PKC modulators bound to the PKCδ-C1b domain in the presence of phospholipid vesicles. The conformationally limited PKC modulator phorbol diacetate (PDAc) is used as an initial test substrate. While unanticipated partitioning of PDAc between an immobilized protein-bound state and a mobile state in the phospholipid assembly was observed, a single conformation in the bound state was identified. In striking contrast, a bryostatin analogue (bryolog) was found to exist exclusively in a protein-bound state, but adopts a distribution of conformations as defined by three independent distance measurements. The detection of multiple PKCδ-C1b-bound bryolog conformers in a functionally relevant phospholipid complex reveals the inherent dynamic nature of cellular systems that is not captured with single-conformation static structures. These results indicate that binding, selectivity, and function of PKC modulators, as well as the design of new modulators, are best addressed using a dynamic multistate model, an analysis potentially applicable to other membrane-associated proteins.
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Affiliation(s)
- Hao Yang
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Daryl Staveness
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven M. Ryckbosch
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alison D. Axtman
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Brian A. Loy
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alexander B. Barnes
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Vijay S. Pande
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jacob Schaefer
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Paul A. Wender
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Chemical and Systems Biology, Stanford
University, Stanford, California 94305, United States
| | - Lynette Cegelski
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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17
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Yamamoto E. Computational and theoretical approaches for studies of a lipid recognition protein on biological membranes. Biophys Physicobiol 2017; 14:153-160. [PMID: 29159013 PMCID: PMC5689545 DOI: 10.2142/biophysico.14.0_153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/26/2017] [Indexed: 01/13/2023] Open
Abstract
Many cellular functions, including cell signaling and related events, are regulated by the association of peripheral membrane proteins (PMPs) with biological membranes containing anionic lipids, e.g., phosphatidylinositol phosphate (PIP). This association is often mediated by lipid recognition modules present in many PMPs. Here, I summarize computational and theoretical approaches to investigate the molecular details of the interactions and dynamics of a lipid recognition module, the pleckstrin homology (PH) domain, on biological membranes. Multiscale molecular dynamics simulations using combinations of atomistic and coarse-grained models yielded results comparable to those of actual experiments and could be used to elucidate the molecular mechanisms of the formation of protein/lipid complexes on membrane surfaces, which are often difficult to obtain using experimental techniques. Simulations revealed some modes of membrane localization and interactions of PH domains with membranes in addition to the canonical binding mode. In the last part of this review, I address the dynamics of PH domains on the membrane surface. Local PIP clusters formed around the proteins exhibit anomalous fluctuations. This dynamic change in protein-lipid interactions cause temporally fluctuating diffusivity of proteins, i.e., the short-term diffusivity of the bound protein changes substantially with time, and may in turn contribute to the formation/dissolution of protein complexes in membranes.
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Affiliation(s)
- Eiji Yamamoto
- Graduate School of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
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18
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Ohashi N, Kobayashi R, Nomura W, Kobayakawa T, Czikora A, Herold BK, Lewin NE, Blumberg PM, Tamamura H. Synthesis and Evaluation of Dimeric Derivatives of Diacylglycerol-Lactones as Protein Kinase C Ligands. Bioconjug Chem 2017; 28:2135-2144. [PMID: 28671468 DOI: 10.1021/acs.bioconjchem.7b00299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein kinase C (PKC) mediates a central cellular signal transduction pathway involved in disorders such as cancer and Alzheimer's disease. PKC is regulated by binding of the second messenger sn-1,2-diacylglycerol (DAG) to its tandem C1 domains, designated C1a and C1b, leading both to PKC activation and to its translocation to the plasma membrane and to internal organelles. Depending on the isoform, there may be differences in the ligand selectivity of the C1a and C1b domains, and there is different spacing between the C1 domains of the conventional and novel PKCs. Bivalent ligands have the potential to exploit these differences between isoforms, yielding isoform selectivity. In the present study, we describe the synthesis of a series of dimeric derivatives of conformationally constrained diacylglycerol (DAG) analogs (DAG-lactones). We characterize the derivatives in vitro for their binding affinities, both to a single C1 domain (the C1b domain of PKCδ) as well as to the conventional PKCα isoform and the novel PKCδ isoform, and we measure their abilities to cause translocation of PKCδ and PKCε in intact cells. The dimeric compound with the 10-carbon linker was modestly more effective for the isolated PKCδ C1b domain than was the monomeric compound. For the intact PKCα and PKCδ, the shortest DAG-lactone dimer had similar affinity to the monomer and affinity decreased progressively up to the 16-carbon linker. The dimeric derivatives did not cause the Golgi accumulation of PKCδ. The present results provide important insights into the development of new chemical tools for biological studies on PKC.
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Affiliation(s)
- Nami Ohashi
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University , 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Ryosuke Kobayashi
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University , 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Wataru Nomura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University , 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuya Kobayakawa
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University , 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Agnes Czikora
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Brienna K Herold
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Nancy E Lewin
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Hirokazu Tamamura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University , 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
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19
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Stewart MD, Igumenova TI. Toggling of Diacylglycerol Affinity Correlates with Conformational Plasticity in C1 Domains. Biochemistry 2017; 56:2637-2640. [PMID: 28505428 DOI: 10.1021/acs.biochem.7b00228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conserved homology-1 (C1) domains are peripheral membrane domains that target their host proteins to diacylglycerol (DAG)-containing membranes. It has been previously shown that a conservative aromatic mutation of a single residue in the C1 domain has a profound effect on DAG affinity. We report that the "DAG-toggling" mutation changes the conformational dynamics of the loop region that forms the binding site for the C1 activators. Moreover, there is a correlation among the residue identity at the mutation site, DAG affinity, and loop dynamics in four C1 variants. We propose that "toggling" of DAG affinity may occur through modulation of both protein-membrane interactions and the geometry of the activator-binding cleft, with the loop dynamics being responsible for the latter.
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Affiliation(s)
- Mikaela D Stewart
- Department of Biochemistry and Biophysics, Texas A&M University , College Station, Texas 77843, United States
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University , College Station, Texas 77843, United States
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20
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Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes. Nat Commun 2017; 8:6. [PMID: 28232750 PMCID: PMC5431895 DOI: 10.1038/s41467-016-0015-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 11/17/2016] [Indexed: 01/13/2023] Open
Abstract
Bryostatin is in clinical trials for Alzheimer’s disease, cancer, and HIV/AIDS eradication. It binds to protein kinase C competitively with diacylglycerol, the endogenous protein kinase C regulator, and plant-derived phorbol esters, but each ligand induces different activities. Determination of the structural origin for these differing activities by X-ray analysis has not succeeded due to difficulties in co-crystallizing protein kinase C with relevant ligands. More importantly, static, crystal-lattice bound complexes do not address the influence of the membrane on the structure and dynamics of membrane-associated proteins. To address this general problem, we performed long-timescale (400–500 µs aggregate) all-atom molecular dynamics simulations of protein kinase C–ligand–membrane complexes and observed that different protein kinase C activators differentially position the complex in the membrane due in part to their differing interactions with waters at the membrane inner leaf. These new findings enable new strategies for the design of simpler, more effective protein kinase C analogs and could also prove relevant to other peripheral protein complexes. Natural supplies of bryostatin, a compound in clinical trials for Alzheimer’s disease, cancer, and HIV, are scarce. Here, the authors perform molecular dynamics simulations to understand how bryostatin interacts with membrane-bound protein kinase C, offering insights for the design of bryostatin analogs.
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21
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Madsen J, Sinitskiy AV, Li J, Voth GA. Highly Coarse-Grained Representations of Transmembrane Proteins. J Chem Theory Comput 2017; 13:935-944. [PMID: 28043122 PMCID: PMC5312841 DOI: 10.1021/acs.jctc.6b01076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Indexed: 01/04/2023]
Abstract
Numerous biomolecules and biomolecular complexes, including transmembrane proteins (TMPs), are symmetric or at least have approximate symmetries. Highly coarse-grained models of such biomolecules, aiming at capturing the essential structural and dynamical properties on resolution levels coarser than the residue scale, must preserve the underlying symmetry. However, making these models obey the correct physics is in general not straightforward, especially at the highly coarse-grained resolution where multiple (∼3-30 in the current study) amino acid residues are represented by a single coarse-grained site. In this paper, we propose a simple and fast method of coarse-graining TMPs obeying this condition. The procedure involves partitioning transmembrane domains into contiguous segments of equal length along the primary sequence. For the coarsest (lowest-resolution) mappings, it turns out to be most important to satisfy the symmetry in a coarse-grained model. As the resolution is increased to capture more detail, however, it becomes gradually more important to match modular repeats in the secondary structure (such as helix-loop repeats) instead. A set of eight TMPs of various complexity, functionality, structural topology, and internal symmetry, representing different classes of TMPs (ion channels, transporters, receptors, adhesion, and invasion proteins), has been examined. The present approach can be generalized to other systems possessing exact or approximate symmetry, allowing for reliable and fast creation of multiscale, highly coarse-grained mappings of large biomolecular assemblies.
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Affiliation(s)
| | | | | | - Gregory A. Voth
- Department of Chemistry,
Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
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22
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Binding mode prediction of aplysiatoxin, a potent agonist of protein kinase C, through molecular simulation and structure–activity study on simplified analogs of the receptor-recognition domain. Bioorg Med Chem 2016; 24:4218-4227. [DOI: 10.1016/j.bmc.2016.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 01/27/2023]
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23
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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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24
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Lum MA, Barger CJ, Hsu AH, Leontieva OV, Black AR, Black JD. Protein Kinase Cα (PKCα) Is Resistant to Long Term Desensitization/Down-regulation by Prolonged Diacylglycerol Stimulation. J Biol Chem 2016; 291:6331-46. [PMID: 26769967 DOI: 10.1074/jbc.m115.696211] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Indexed: 11/06/2022] Open
Abstract
Sustained activation of PKCα is required for long term physiological responses, such as growth arrest and differentiation. However, studies with pharmacological agonists (e.g. phorbol 12-myristate 13-acetate (PMA)) indicate that prolonged stimulation leads to PKCα desensitization via dephosphorylation and/or degradation. The current study analyzed effects of chronic stimulation with the physiological agonist diacylglycerol. Repeated addition of 1,2-dioctanoyl-sn-glycerol (DiC8) resulted in sustained plasma membrane association of PKCα in a pattern comparable with that induced by PMA. However, although PMA potently down-regulated PKCα, prolonged activation by DiC8 failed to engage known desensitization mechanisms, with the enzyme remaining membrane-associated and able to support sustained downstream signaling. DiC8-activated PKCα did not undergo dephosphorylation, ubiquitination, or internalization, early events in PKCα desensitization. Although DiC8 efficiently down-regulated novel PKCs PKCδ and PKCϵ, differences in Ca(2+) sensitivity and diacylglycerol affinity were excluded as mediators of the selective resistance of PKCα. Roles for Hsp/Hsc70 and Hsp90 were also excluded. PMA, but not DiC8, targeted PKCα to detergent-resistant membranes, and disruption of these domains with cholesterol-binding agents demonstrated a role for differential membrane compartmentalization in selective agonist-induced degradation. Chronic DiC8 treatment failed to desensitize PKCα in several cell types and did not affect PKCβI; thus, conventional PKCs appear generally insensitive to desensitization by sustained diacylglycerol stimulation. Consistent with this conclusion, prolonged (several-day) membrane association/activation of PKCα is seen in self-renewing epithelium of the intestine, cervix, and skin. PKCα deficiency affects gene expression, differentiation, and tumorigenesis in these tissues, highlighting the importance of mechanisms that protect PKCα from desensitization in vivo.
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Affiliation(s)
- Michelle A Lum
- From the Eppley Institute for Research in Cancer and Allied Diseases and the Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198-5950 and the Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Carter J Barger
- From the Eppley Institute for Research in Cancer and Allied Diseases and the Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198-5950 and
| | - Alice H Hsu
- From the Eppley Institute for Research in Cancer and Allied Diseases and the Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198-5950 and
| | - Olga V Leontieva
- the Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Adrian R Black
- From the Eppley Institute for Research in Cancer and Allied Diseases and the Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198-5950 and the Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York 14263
| | - Jennifer D Black
- From the Eppley Institute for Research in Cancer and Allied Diseases and the Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198-5950 and the Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York 14263
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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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Thangsunan P, Tateing S, Hannongbua S, Suree N. Structural insights into the interactions of phorbol ester and bryostatin complexed with protein kinase C: a comparative molecular dynamics simulation study. J Biomol Struct Dyn 2015; 34:1561-75. [PMID: 26292580 DOI: 10.1080/07391102.2015.1084479] [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] [Indexed: 10/23/2022]
Abstract
Protein kinase C (PKC) isozymes are important regulatory enzymes that have been implicated in many diseases, including cancer, Alzheimer's disease, and in the eradication of HIV/AIDS. Given their potential clinical ramifications, PKC modulators, e.g. phorbol esters and bryostatin, are also of great interest in the drug development. However, structural details on the binding between PKC and its modulators, especially bryostatin - the highly potent and non-tumor promoting activator for PKCs, are still lacking. Here, we report the first comparative molecular dynamics study aimed at gaining structural insight into the mechanisms by which the PKC delta cys2 activator domain is used in its binding to phorbol ester and bryostatin-1. As anticipated in the phorbol ester binding, hydrogen bonds are formed through the backbone atoms of Thr242, Leu251, and Gly253 of PKC. However, the opposition of H-bond formation between Thr242 and Gly253 may cause the phorbol ester complex to become less stable when compared with the bryostatin binding. For the PKC delta-bryostatin complex, hydrogen bonds are formed between the Gly253 backbone carbonyl and the C30 carbomethoxy substituent of the ligand. Additionally, the indole Nε1 of the highly homologous Trp252 also forms an H-bond to the C20 ester group on bryostatin. Backbone fluctuations also suggest that this latter H-bond formation may abrogate the transient interaction between Trp252 and His269, thus dampening the fluctuations observed on the nearby Zn(2+)-coordinating residues. This new dynamic fluctuation dampening model can potentially benefit future design of new PKC modulators.
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Affiliation(s)
- Patcharapong Thangsunan
- a Graduate Program in Biotechnology , The Graduate School, Chiang Mai University , 239 Huay Kaew Rd, Suthep, Muang, Chiang Mai 50200 , Thailand.,b Faculty of Science, Department of Chemistry, Division of Biochemistry and Biochemical Technology , Chiang Mai University , 239 Huay Kaew Rd, Suthep, Muang, Chiang Mai 50200 , Thailand
| | - Suriya Tateing
- a Graduate Program in Biotechnology , The Graduate School, Chiang Mai University , 239 Huay Kaew Rd, Suthep, Muang, Chiang Mai 50200 , Thailand.,b Faculty of Science, Department of Chemistry, Division of Biochemistry and Biochemical Technology , Chiang Mai University , 239 Huay Kaew Rd, Suthep, Muang, Chiang Mai 50200 , Thailand
| | - Supa Hannongbua
- c Faculty of Science, Department of Chemistry , Kasetsart University , Bangkok 10900 , Thailand
| | - Nuttee Suree
- b Faculty of Science, Department of Chemistry, Division of Biochemistry and Biochemical Technology , Chiang Mai University , 239 Huay Kaew Rd, Suthep, Muang, Chiang Mai 50200 , Thailand
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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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Borah R, Mamidi N, Panda S, Gorai S, Pathak SK, Manna D. Elucidating the interaction of γ-hydroxymethyl-γ-butyrolactone substituents with model membranes and protein kinase C-C1 domains. MOLECULAR BIOSYSTEMS 2015; 11:1389-99. [PMID: 25820877 DOI: 10.1039/c5mb00100e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protein kinase C (PKC) family of proteins is an attractive drug target. Dysregulation of PKC-dependent signalling pathways is related to several human diseases like cancer, immunological and other diseases. We approached the problem of altering PKC activities by developing C1 domain-based PKC ligands. In this report γ-hydroxymethyl-γ-butyrolactone (HGL) substituents were investigated in an effort to develop small molecule-based PKC regulators with higher specificity for C1 domain than the endogenous diacylglycerols (DAGs). Extensive analysis of membrane-ligands interaction measurements revealed that the membrane-active compounds strongly interact with the lipid bilayers and the hydrophilic parts of compounds localize at the bilayer/water interface. The pharmacophores like hydroxymethyl, carbonyl groups and acyl-chain length of the compounds are crucial for their interaction with the C1 domain proteins. The potent compounds showed more than 17-fold stronger binding affinity for the C1 domains than DAG under similar experimental conditions. Nonradioactive kinase assay confirmed that these potent compounds have similar or better PKC dependent phosphorylation capabilities than DAG under similar experimental conditions. Hence, our findings reveal that these HGL analogues represent an attractive group of structurally simple C1 domain ligands that can be further structurally altered to improve their potencies.
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Affiliation(s)
- Rituparna Borah
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India.
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29
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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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