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Abstract
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Membrane
lipids interact with proteins in a variety of ways, ranging
from providing a stable membrane environment for proteins to being
embedded in to detailed roles in complicated and well-regulated protein
functions. Experimental and computational advances are converging
in a rapidly expanding research area of lipid–protein interactions.
Experimentally, the database of high-resolution membrane protein structures
is growing, as are capabilities to identify the complex lipid composition
of different membranes, to probe the challenging time and length scales
of lipid–protein interactions, and to link lipid–protein
interactions to protein function in a variety of proteins. Computationally,
more accurate membrane models and more powerful computers now enable
a detailed look at lipid–protein interactions and increasing
overlap with experimental observations for validation and joint interpretation
of simulation and experiment. Here we review papers that use computational
approaches to study detailed lipid–protein interactions, together
with brief experimental and physiological contexts, aiming at comprehensive
coverage of simulation papers in the last five years. Overall, a complex
picture of lipid–protein interactions emerges, through a range
of mechanisms including modulation of the physical properties of the
lipid environment, detailed chemical interactions between lipids and
proteins, and key functional roles of very specific lipids binding
to well-defined binding sites on proteins. Computationally, despite
important limitations, molecular dynamics simulations with current
computer power and theoretical models are now in an excellent position
to answer detailed questions about lipid–protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Besian I Sejdiu
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haydee Mesa-Galloso
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
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Abstract
Polyunsaturated fatty acids (PUFAs) act on most ion channels, thereby having significant physiological and pharmacological effects. In this review we summarize data from numerous PUFAs on voltage-gated ion channels containing one or several voltage-sensor domains, such as voltage-gated sodium (NaV), potassium (KV), calcium (CaV), and proton (HV) channels, as well as calcium-activated potassium (KCa), and transient receptor potential (TRP) channels. Some effects of fatty acids appear to be channel specific, whereas others seem to be more general. Common features for the fatty acids to act on the ion channels are at least two double bonds in cis geometry and a charged carboxyl group. In total we identify and label five different sites for the PUFAs. PUFA site 1: The intracellular cavity. Binding of PUFA reduces the current, sometimes as a time-dependent block, inducing an apparent inactivation. PUFA site 2: The extracellular entrance to the pore. Binding leads to a block of the channel. PUFA site 3: The intracellular gate. Binding to this site can bend the gate open and increase the current. PUFA site 4: The interface between the extracellular leaflet of the lipid bilayer and the voltage-sensor domain. Binding to this site leads to an opening of the channel via an electrostatic attraction between the negatively charged PUFA and the positively charged voltage sensor. PUFA site 5: The interface between the extracellular leaflet of the lipid bilayer and the pore domain. Binding to this site affects slow inactivation. This mapping of functional PUFA sites can form the basis for physiological and pharmacological modifications of voltage-gated ion channels.
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Affiliation(s)
- Fredrik Elinder
- Department of Clinical and Experimental Medicine, Linköping University Linköping, Sweden
| | - Sara I Liin
- Department of Clinical and Experimental Medicine, Linköping University Linköping, Sweden
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Ramakrishnan N, Sunil Kumar PB, Radhakrishnan R. Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins. Phys Rep 2014; 543:1-60. [PMID: 25484487 PMCID: PMC4251917 DOI: 10.1016/j.physrep.2014.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Biological membranes constitute boundaries of cells and cell organelles. These membranes are soft fluid interfaces whose thermodynamic states are dictated by bending moduli, induced curvature fields, and thermal fluctuations. Recently, there has been a flood of experimental evidence highlighting active roles for these structures in many cellular processes ranging from trafficking of cargo to cell motility. It is believed that the local membrane curvature, which is continuously altered due to its interactions with myriad proteins and other macromolecules attached to its surface, holds the key to the emergent functionality in these cellular processes. Mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the protein, shape and amino acid composition of the protein, and its amino acid contents. The specificity of molecular interactions together with the cooperativity of multiple proteins induce and stabilize complex membrane shapes at the mesoscale. These shapes span a wide spectrum ranging from the spherical plasma membrane to the complex cisternae of the Golgi apparatus. Mapping the relation between the protein-induced deformations at the molecular scale and the resulting mesoscale morphologies is key to bridging cellular experiments across the various length scales. In this review, we focus on the theoretical and computational methods used to understand the phenomenology underlying protein-driven membrane remodeling. Interactions at the molecular scale can be computationally probed by all atom and coarse grained molecular dynamics (MD, CGMD), as well as dissipative particle dynamics (DPD) simulations, which we only describe in passing. We choose to focus on several continuum approaches extending the Canham - Helfrich elastic energy model for membranes to include the effect of curvature-inducing proteins and explore the conformational phase space of such systems. In this description, the protein is expressed in the form of a spontaneous curvature field. The approaches include field theoretical methods limited to the small deformation regime, triangulated surfaces and particle-based computational models to investigate the large-deformation regimes observed in the natural state of many biological membranes. Applications of these methods to understand the properties of biological membranes in homogeneous and inhomogeneous environments of proteins, whose underlying curvature fields are either isotropic or anisotropic, are discussed. The diversity in the curvature fields elicits a rich variety of morphological states, including tubes, discs, branched tubes, and caveola. Mapping the thermodynamic stability of these states as a function of tuning parameters such as concentration and strength of curvature induction of the proteins is discussed. The relative stabilities of these self-organized shapes are examined through free-energy calculations. The suite of methods discussed here can be tailored to applications in specific cellular settings such as endocytosis during cargo trafficking and tubulation of filopodial structures in migrating cells, which makes these methods a powerful complement to experimental studies.
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Affiliation(s)
- N. Ramakrishnan
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA-19104
| | - P. B. Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai, India - 600036
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA-19104
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Horn JN, Kao TC, Grossfield A. Coarse-grained molecular dynamics provides insight into the interactions of lipids and cholesterol with rhodopsin. Adv Exp Med Biol 2014; 796:75-94. [PMID: 24158802 DOI: 10.1007/978-94-007-7423-0_5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein function is a complicated interplay between structure and dynamics, which can be heavily influenced by environmental factors and conditions. This is particularly true in the case of membrane proteins, such as the visual receptor rhodopsin. It has been well documented that lipid headgroups, polyunsaturated tails, and the concentration of cholesterol in membranes all play a role in the function of rhodopsin. Recently, we used all-atom simulations to demonstrate that different lipid species have preferential interactions and possible binding sites on rhodopsin's surface, consistent with experiment. However, the limited timescales of the simulations meant that the statistical uncertainty of these results was substantial. Accordingly, we present here 32 independent 1.6 μs coarse-grained simulations exploring lipids and cholesterols surrounding rhodopsin and opsin, in lipid bilayers mimicking those found naturally. Our results agree with those found experimentally and in previous simulations, but with far better statistical certainty. The results demonstrate the value of combining all-atom and coarse-grained models with experiment to provide a well-rounded view of lipid-protein interactions.
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Affiliation(s)
- Joshua N Horn
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, 712, Rochester, NY, 14642, USA
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Goldman RC. Why are membrane targets discovered by phenotypic screens and genome sequencing in Mycobacterium tuberculosis? Tuberculosis (Edinb) 2013; 93:569-88. [DOI: 10.1016/j.tube.2013.09.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 12/11/2022]
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Heilmann M, Heilmann I. Arranged marriage in lipid signalling? The limited choices of PtdIns(4,5)P2 in finding the right partner. Plant Biol (Stuttg) 2013; 15:789-797. [PMID: 23627419 DOI: 10.1111/plb.12025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/07/2013] [Indexed: 06/02/2023]
Abstract
Inositol-containing phospholipids (phosphoinositides, PIs) control numerous cellular processes in eukaryotic cells. For plants, a key involvement of PIs has been demonstrated in the regulation of membrane trafficking, cytoskeletal dynamics and in processes mediating the adaptation to changing environmental conditions. Phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P(2)) mediates its cellular functions via binding to various alternative target proteins. Such downstream targets of PtdIns(4,5)P(2) are characterised by the possession of specific lipid-binding domains, and binding of the PtdIns(4,5)P(2) ligand exerts effects on their activity or localisation. The large number of potential alternative binding partners - and associated cellular processes - raises the question how alternative or even contrapuntal effects of PtdIns(4,5)P(2) are orchestrated to enable cellular function. This article aims to provide an overview of recent insights and new views on how distinct functional pools of PtdIns(4,5)P(2) are generated and maintained. The emerging picture suggests that PtdIns(4,5)P(2) species containing different fatty acids influence the lateral mobility of the lipids in the membrane, possibly enabling specific interactions of PtdIns(4,5)P(2) pools with certain downstream targets. PtdIns(4,5)P(2) pools with certain functions might also be defined by protein-protein interactions of PI4P 5-kinases, which pass PtdIns(4,5)P(2) only to certain downstream partners. Individually or in combination, PtdIns(4,5)P(2) species and specific protein-protein interactions of PI4P 5-kinases might contribute to the channelling of PtdIns(4,5)P(2) signals towards specific functional effects. The dynamic nature of PI-dependent signalling complexes with specific functions is an added challenge for future studies of plant PI signalling.
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Affiliation(s)
- M Heilmann
- Department of Cellular Biochemistry, Institute for Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.
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Abstract
The interactions between lipids and proteins are crucial for a range of biological processes, from the folding and stability of membrane proteins to signaling and metabolism facilitated by lipid-binding proteins. However, high-resolution structural details concerning functional lipid/protein interactions are scarce due to barriers in both experimental isolation of native lipid-bound complexes and subsequent biophysical characterization. The molecular dynamics (MD) simulation approach provides a means to complement available structural data, yielding dynamic, structural, and thermodynamic data for a protein embedded within a physiologically realistic, modelled lipid environment. In this chapter, we provide a guide to current methods for setting up and running simulations of membrane proteins and soluble, lipid-binding proteins, using standard atomistically detailed representations, as well as simplified, coarse-grained models. In addition, we outline recent studies that illustrate the power of the simulation approach in the context of biologically relevant lipid/protein interactions.
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Affiliation(s)
- Teresa Paramo
- Department of Chemistry, Unilever Centre for Molecular Informatics, University of Cambridge, Cambridge, UK
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Pereira ASA, Padilha RJR, Lima-Filho JL, Chaves MEC. Scanning electron microscopy of the human low-density lipoprotein interaction with the tegument of Schistosoma mansoni. Parasitol Res 2011; 109:1395-402. [PMID: 21503638 DOI: 10.1007/s00436-011-2386-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 04/06/2011] [Indexed: 12/15/2022]
Abstract
The interaction between host molecules and Schistosoma mansoni has been regarded as a key feature for parasite survival. In this work, scanning electron microscopy was used to study the interaction of human low-density lipoprotein (LDL) with the tegument of the adult worm of S. mansoni. Worms were incubated in RPMI 1640 containing 10% of LPDS and 40 μg LDL/mL during 30, 60, and 120 min. Control worms were processed in the same way, without LDL. After the incubations, the samples were fixed and processed to scanning electron microscopy. The results demonstrated interaction of the LDL particles with the male parasite tegument. Male and female worms incubated without LDL from 0 (control) to 120 min did not show alterations in the tegument. It was observed a larger number of LDL particles on the dorsal region of male adult worm than others regions (anterior, posterior and gynecophoral canal). The female tegument did not show adherence of LDL. Aggregates on the tegument of the male worm were in greater number and size in the incubation times of 30 and 60 min than 120 min. The comparison between 30 and 120 min of incubation showed that the particles' size diminished from 2,650-860 nm to 634-363 nm, respectively. Such reduction can be due to the capture and the use of the lipids by the worm. Therefore, the internalization of lipids from LDL by the male worms seems to be a mechanism independent of endocytosis. Differences between males and females suggest lipid transference from male to female through gynecophoral canal.
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Affiliation(s)
- Adriana S A Pereira
- Laboratório de Imunopatologia Prof. Keizo Asami (LIKA), Universidade Federal de Pernambuco, Avenida Professor Moraes Rego, s/n-CEP 50670-901, Recife, Pernambuco, Brazil
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Bond PJ, Guy AT, Heron AJ, Bayley H, Khalid S. Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation. Biochemistry 2011; 50:3777-83. [PMID: 21428458 DOI: 10.1021/bi101404n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein nanopores show great potential as low-cost detectors in DNA sequencing devices. To date, research has largely focused on the staphylococcal pore α-hemolysin (αHL). In the present study, we have developed simplified models of the wild-type αHL pore and various mutants in order to study the translocation dynamics of single-stranded DNA under the influence of an applied electric field. The model nanopores reflect the experimentally measured conductance values in planar lipid bilayers. We show that interactions between rings of cationic amino acids and DNA backbone phosphates result in metastable tethering of nucleic acid molecules within the pore, leading us to propose a "binding and sliding" mechanism for translocation. We also observe folding of DNA into nonlinear conformational intermediates during passage through the confined nanopore environment. Despite adopting nonlinear conformations, the DNA hexamer always exits the pore in the same orientation as it enters (3' to 5') in our simulations. The observations from our simulations help to rationalize experimentally determined trends in residual current and translocation efficiency for αHL and its mutants.
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Affiliation(s)
- Peter J Bond
- Unilever Centre, Department of Chemistry, Lensfield Road, University of Cambridge, Cambridge CB2 1EW, U.K
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D'Avanzo N, Cheng WWL, Wang S, Enkvetchakul D, Nichols CG. Lipids driving protein structure? Evolutionary adaptations in Kir channels. Channels (Austin) 2010; 4:139-41. [PMID: 21150302 DOI: 10.4161/chan.4.3.12129] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Many eukaryotic channels, transporters and receptors are activated by phosphatidyl inositol bisphosphate (PIP(2)) in the membrane, and every member of the eukaryotic inward rectifier potassium (Kir) channel family requires membrane PIP(2) for activity. In contrast, a bacterial homolog (KirBac1.1) is specifically inhibited by PIP(2). We speculate that a key evolutionary adaptation in eukaryotic channels is the insertion of additional linkers between transmembrane and cytoplasmic domains, revealed by new crystal structures, that convert PIP(2) inhibition to activation. Such an adaptation may reflect a novel evolutionary drive to protein structure, and that was necessary to permit channel function within the highly negatively charged membranes that evolved in the eukaryotic lineage.
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Affiliation(s)
- Nazzareno D'Avanzo
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
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13
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Abstract
Recent advances in molecular dynamics (MD) simulation methods and in available computational resources have allowed for more reliable simulations of biological phenomena. From all-atom MD simulations, we are now able to visualize in detail the interactions between antimicrobial peptides (AMPs) and a variety of membrane mimics. This helps us to understand the molecular mechanisms of antimicrobial activity and toxicity. This chapter describes how to set up and conduct molecular dynamics simulations of AMPs and membrane mimics. Details are given for the construction of systems of interest for studying AMPs, which can include simulations of peptides in water, micelles, or lipid bilayers. Explanations of the parameters needed for running a simulation are provided as well.
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Sen M, Herzik M, Craft JW, Creath AL, Agrawal S, Ruf W, Legge GB. Spectroscopic Characterization of Successive Phosphorylation of the Tissue Factor Cytoplasmic Region. ACTA ACUST UNITED AC 2009; 3:58-64. [PMID: 20076769 DOI: 10.2174/1874383800903010058] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tissue Factor (TF) is well known for its role during the activation of the coagulation pathway, but it is also critical for tumor biology and inflammation through protease activated receptor (PAR) 2 signaling. This signaling function is modulated by the successive phosphorylation of residues Ser253 and Ser258 within the TF cytoplasmic region (TFCR). This paper reports how we used NMR and spectroscopic methods to investigate the structural propensities of the unphosphorylated and phosphorylated forms of the TFCR. When unphosphorylated, the TFCR forms a local hydrophobic collapse around Trp254 and an electropositive patch from the membrane proximal basic block (Arg246-Lys247) to the conserved PKCalpha consensus residue Lys255. Phosphorylation of Ser253 alters the charge characteristics of this membrane proximal region, thereby strengthening the interaction between residue Ala248 and the Trp254 aromatic group. Phosphorylation of the Ser258-Pro259 motif destabilizes a turn at the C-terminus to form an extended polyproline helical motif. Our data suggests that by changing both its charge and local structural propensity, covalent modifications of the TFCR can potentially regulate its association with the cellular membrane and its signaling partners.
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Affiliation(s)
- Mehmet Sen
- University of Houston, Department of Biology and Biochemistry, Houston, TX 77204-5001, USA
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van der Kamp MW, Shaw KE, Woods CJ, Mulholland AJ. Biomolecular simulation and modelling: status, progress and prospects. J R Soc Interface 2008; 5 Suppl 3:S173-90. [PMID: 18611844 PMCID: PMC2706107 DOI: 10.1098/rsif.2008.0105.focus] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 06/05/2008] [Accepted: 06/06/2008] [Indexed: 11/12/2022] Open
Abstract
Molecular simulation is increasingly demonstrating its practical value in the investigation of biological systems. Computational modelling of biomolecular systems is an exciting and rapidly developing area, which is expanding significantly in scope. A range of simulation methods has been developed that can be applied to study a wide variety of problems in structural biology and at the interfaces between physics, chemistry and biology. Here, we give an overview of methods and some recent developments in atomistic biomolecular simulation. Some recent applications and theoretical developments are highlighted.
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Affiliation(s)
| | | | | | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of BristolBristol BS8 1TS, UK
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Abstract
The KcsA potassium channel from Streptomyces lividans is one of the most actively studied ion channels. However, there are still unresolved issues about its gating mechanism in vivo because the channel is only activated by highly acidic intracellular pH, meaning that it will be mostly inactive in its host environment. In this study we have used a genetic complementation assay of K+-auxotrophic E. coli (TK2420) and S. cerevisiae (SGY1528) to identify activatory or 'gain-of-function' mutations which allow functional activity of KcsA in the physiological environment of two markedly different expression systems. These mutations clustered at the helix-bundle-crossing in both TM1 and TM2 (residues H25, L105, A108, T112, W113, F114, E118 and Q119), and include residues previously implicated in the pH-gating mechanism. We discuss how these gain-of-function mutations may result in their activatory phenotype, the relative merits of the E. coli and S. cerevisiae genetic complementation approaches for the identification of gating mutations in prokaryotic K+ channels, and ways in which this assay may be improved for future use in screening protocols.
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Affiliation(s)
- Jennifer J Paynter
- Oxford Centre for Gene Function, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
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Kunji ERS, Harding M, Butler PJG, Akamine P. Determination of the molecular mass and dimensions of membrane proteins by size exclusion chromatography. Methods 2008; 46:62-72. [PMID: 18952172 DOI: 10.1016/j.ymeth.2008.10.020] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 10/09/2008] [Accepted: 10/16/2008] [Indexed: 11/18/2022] Open
Abstract
Size exclusion chromatography is an established technique for the determination of hydrodynamic volumes of proteins or protein complexes. When applied to membrane proteins, the contribution of the detergent micelle, which is required to keep the protein soluble in the aqueous phase, needs to be determined to obtain accurate measurements for the protein. In a detergent series, in which the detergents differ only by the length of the alkyl chain, the contribution of the detergent micelle to the hydrodynamic volume is variable, whereas the contribution of the protein is constant. By using this approach, several parameters of membrane proteins can be estimated by extrapolation, such as the radius at the midpoint of the membrane, the average radius, the Stokes radius, and the excluded volume. The molecular mass of the protein can be determined by two independent measurements that arise from the behaviour of the free detergent micelle and protein-detergent micelle during size exclusion chromatography and the determination of the detergent-protein ratio. Determining the dimensions of protein-detergent micelles may facilitate membrane protein purification and crystallization by defining the accessibility of the protein surface.
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Affiliation(s)
- Edmund R S Kunji
- The Medical Research Council, Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 0XY, UK.
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Mace OJ, Woollhead AM, Baines DL. AICAR activates AMPK and alters PIP2 association with the epithelial sodium channel ENaC to inhibit Na+ transport in H441 lung epithelial cells. J Physiol 2008; 586:4541-57. [PMID: 18669532 DOI: 10.1113/jphysiol.2008.158253] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Changes in amiloride-sensitive epithelial Na(+) channel (ENaC) activity (NP(o)) in the lung lead to pathologies associated with dysregulation of lung fluid balance. UTP activation of purinergic receptors and hydrolysis of PIP(2) via activation of phospholipase C (PLC) or AICAR activation of AMP-activated protein kinase (AMPK) inhibited amiloride-sensitive Na(+) transport across human H441 epithelial cell monolayers. Neither treatment altered alpha, beta or gamma ENaC subunit abundance (N) in the apical membrane indicating that the mechanism of inhibition was via a change in channel open state probability (P(o)). We found that UTP depleted PIP(2) abundance in the apical membrane whilst activation of AMPK prevented the binding of beta and gamma ENaC subunits to PIP(2.) The association of PIP(2) with the ENaC subunits is required to maintain channel activity via P(o). Thus, these data show for the first time that AICAR activation of AMPK inhibits Na(+) transport via a mechanism that perturbs the PIP(2)-ENaC channel interaction to alter P(o). In addition, we show that dissociation of PIP(2) from ENaC together with activation of AMPK further reduced Na(+) transport by a secondary effect that correlated with ENaC subunit internalization. Thus, when PIP(2)-ENaC subunit interactions were compromised, ENaC protein retrieval was initiated, indicating that AMPK can modulate ENaC P(o) and N.
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Affiliation(s)
- Oliver J Mace
- Division of Basic Medical Sciences, St George's University of London, Cranmer Terrace, London SW17 0RE, UK.
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Abstract
Connexins are plasma membrane proteins that associate in hexameric complexes to form channels named connexons. Two connexons in neighboring cells may dock to form a "gap junction" channel, i.e. an intercellular conduit that permits the direct exchange of solutes between the cytoplasm of adjacent cells and thus mediate cell-cell ion and metabolic signaling. The lack of high resolution data for connexon structures has hampered so far the study of the structure-function relationships that link molecular effects of disease-causing mutations with their observed phenotypes. Here we present a combination of modeling techniques and molecular dynamics (MD) to infer side chain positions starting from low resolution structures containing only C alpha atoms. We validated this procedure on the structure of the KcsA potassium channel, which is solved at atomic resolution. We then produced a fully atomistic model of a homotypic Cx32 connexon starting from a published model of the C alpha carbons arrangement for the connexin transmembrane helices, to which we added extracellular and cytoplasmic loops. To achieve structural relaxation within a realistic environment, we used MD simulations inserted in an explicit solvent-membrane context and we subsequently checked predictions of putative side chain positions and interactions in the Cx32 connexon against a vast body of experimental reports. Our results provide new mechanistic insights into the effects of numerous spontaneous mutations and their implication in connexin-related pathologies. This model constitutes a step forward towards a structurally detailed description of the gap junction architecture and provides a structural platform to plan new biochemical and biophysical experiments aimed at elucidating the structure of connexin channels and hemichannels.
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Affiliation(s)
- Sergio Pantano
- Institut Pasteur of Montevideo, Montevideo, Uruguay
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Rome, Italy
| | - Francesco Zonta
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Rome, Italy
| | - Fabio Mammano
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Rome, Italy
- Dipartimento di Fisica “G.Galilei”, Università di Padova, Padova, Italy
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Wee CL, Balali-Mood K, Gavaghan D, Sansom MS. The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations. Biophys J 2008; 95:1649-57. [PMID: 18469074 DOI: 10.1529/biophysj.107.123190] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A number of membrane-active enzymes act in a complex environment formed by the interface between a lipid bilayer and bulk water. Although x-ray diffraction studies yield structures of isolated enzyme molecules, a detailed characterization of their interactions with the interface requires a measure of how deeply such a membrane-associated protein penetrates into a lipid bilayer. Here, we apply coarse-grained (CG) molecular dynamics (MD) simulations to probe the interaction of porcine pancreatic phospholipase A2 (PLA2) with a lipid bilayer containing palmitoyl-oleoyl-phosphatidyl choline and palmitoyl-oleoyl-phosphatidyl glycerol molecules. We also used a configuration from a CG-MD trajectory to initiate two atomistic (AT) MD simulations. The results of the CG and AT simulations are evaluated by comparison with available experimental data. The membrane-binding surface of PLA2 consists of a patch of hydrophobic residues surrounded by polar and basic residues. We show this proposed footprint interacts preferentially with the anionic headgroups of the palmitoyl-oleoyl-phosphatidyl glycerol molecules. Thus, both electrostatic and hydrophobic interactions determine the location of PLA2 relative to the bilayer. From a general perspective, this study demonstrates that CG-MD simulations may be used to reveal the orientation and location of a membrane-surface-bound protein relative to a lipid bilayer, which may subsequently be refined by AT-MD simulations to probe more detailed interactions.
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Abstract
Phosphatidylinositol 4,5-bisphosphate (PIP2) is a minority phospholipid of the inner leaflet of plasma membranes. Many plasma membrane ion channels and ion transporters require PIP2 to function and can be turned off by signaling pathways that deplete PIP2. This review discusses the dependence of ion channels on phosphoinositides and considers possible mechanisms by which PIP2 and analogues regulate ion channel activity.
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Affiliation(s)
- Byung-Chang Suh
- Department of Physiology and Biophysics University of Washington School of Medicine, Seattle, Washington 98195
| | - Bertil Hille
- Department of Physiology and Biophysics University of Washington School of Medicine, Seattle, Washington 98195
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Haider S, Tarasov AI, Craig TJ, Sansom MSP, Ashcroft FM. Identification of the PIP2-binding site on Kir6.2 by molecular modelling and functional analysis. EMBO J 2007; 26:3749-59. [PMID: 17673911 PMCID: PMC1952224 DOI: 10.1038/sj.emboj.7601809] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 07/03/2007] [Indexed: 12/25/2022] Open
Abstract
ATP-sensitive potassium (K(ATP)) channels couple cell metabolism to electrical activity by regulating K(+) fluxes across the plasma membrane. Channel closure is facilitated by ATP, which binds to the pore-forming subunit (Kir6.2). Conversely, channel opening is potentiated by phosphoinositol bisphosphate (PIP(2)), which binds to Kir6.2 and reduces channel inhibition by ATP. Here, we use homology modelling and ligand docking to identify the PIP(2)-binding site on Kir6.2. The model is consistent with a large amount of functional data and was further tested by mutagenesis. The fatty acyl tails of PIP(2) lie within the membrane and the head group extends downwards to interact with residues in the N terminus (K39, N41, R54), transmembrane domains (K67) and C terminus (R176, R177, E179, R301) of Kir6.2. Our model suggests how PIP(2) increases channel opening and decreases ATP binding and channel inhibition. It is likely to be applicable to the PIP(2)-binding site of other Kir channels, as the residues identified are conserved and influence PIP(2) sensitivity in other Kir channel family members.
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Affiliation(s)
- Shozeb Haider
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Tim J Craig
- Laboratory of Physiology, University of Oxford, Oxford, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Frances M Ashcroft
- Laboratory of Physiology, University of Oxford, Oxford, UK
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK. Tel.: +44 1865 285810; Fax: +44 1865 285811; E-mail:
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Abstract
The mechanosensitive channel of small conductance (MscS) belongs to a family of membrane proteins that are gated in response to changes in membrane tension, thereby protecting the cell from hypo-osmotic shock. Here we report on passive ion transport simulations of MscS in a POPC bilayer using a coarse-grained particle-based description based on the Boltzmann transport Monte Carlo method. Single channel current-voltage curves are computed over hundreds of nanoseconds for channel conformations derived from all-atom molecular dynamics simulations reaching an overall simulation time of over 5 micros. Channel conformations similar to that of the crystal structure exhibit low conductance, whereas conformations reached after opening the channel by means of steered molecular dynamics simulations match experimentally determined conductances. However, while experiments indicate a slight preference for anionic currents, the simulated channel strongly selects anions over cations and the direction of rectification at high voltages is opposite to what is observed in experiments. Three-dimensional maps of time-averaged ion distribution and equilibrium occupancy profiles constructed from trajectory data indicate separation of anions and cations inside and in the immediate vicinity of the large cytoplasmic domain of MscS, in accordance with earlier molecular dynamics simulations. This separation arises from the distribution of ionizable residues of MscS and suggests a specific, yet unknown, functional purpose.
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Affiliation(s)
- Marcos Sotomayor
- Department of Physics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA
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