1
|
Molecular dynamics simulations of homo-oligomeric bundles embedded within a lipid bilayer. Biophys J 2014; 105:1569-80. [PMID: 24094398 DOI: 10.1016/j.bpj.2013.07.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 07/12/2013] [Accepted: 07/15/2013] [Indexed: 11/23/2022] Open
Abstract
Using molecular dynamics simulations, we studied the structure, interhelix interactions, and dynamics of transmembrane proteins. Specifically, we investigated homooligomeric helical bundle systems consisting of synthetic α-helices with either the sequence Ac-(LSLLLSL)3-NH2 (LS2) or Ac-(LSSLLSL)3-NH2 (LS3). The LS2 and LS3 helical peptides are designed to have amphipathic characteristics that form ion channels in membrane. We simulated bundles containing one to six peptides that were embedded in palmitoyl-oleoyl-phosphatidylcholine (POPC) lipid bilayer and placed between two lamellae of water. We aim to provide a fundamental understanding of how amphipathic helical peptides interact with each other and their dynamical behaviors in different homooligomeric states. To understand structural properties, we examined the helix lengths, tilt angles of individual helices and the entire bundle, interhelix distances, interhelix cross-angles, helix hydrophobic-to-hydrophilic vector projections, and the average number of interhelix hydrophilic (serine-serine) contacts lining the pore of the transmembrane channel. To analyze dynamical properties, we calculated the rotational autocorrelation function of each helix and the cross-correlation of the rotational velocity between adjacent helices. The observed structural and dynamical characteristics show that higher order bundles containing four to six peptides are composed of multiple lower order bundles of one to three peptides. For example, the LS2 channel was found to be stable in a tetrameric bundle composed of a "dimer of dimers." In addition, we observed that there is a minimum of two strong hydrophilic contacts between a pair of adjacent helices in the dimer to tetramer systems and only one strong hydrophilic interhelix contact in helix pairs of the pentamer and hexamer systems. We believe these results are general and can be applied to more complex ion channels, providing insight into ion channel stability and assembly.
Collapse
|
2
|
Devi U, Brown JRD, Almond A, Webb SJ. Pd(II)-mediated assembly of porphyrin channels in bilayer membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:1448-1456. [PMID: 21174428 DOI: 10.1021/la104152s] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A membrane-spanning bis(meso-3-pyridyl) porphyrin 1 has been synthesized, embedded in EYPC vesicles, and upon Pd(II) addition has been shown to form ionophores that allow the passage of anionic 5/6-carboxyfluorescein through membranes. The geometric matching of bis(meso-3-pyridyl) porphyrin 1 and trans-Pd(II) was designed to give a cyclic porphyrin trimer [PdCl(2)(1)](3). However, solution-phase studies showed that PdCl(2)(PhCN)(2) cross linked 1 into linear oligomers at porphyrin concentrations above 10 mM, although the formation of cyclic species was inferred from studies at concentrations below 2 μM. Fluorescence titrations showed that embedding porphyrin 1 in bilayers greatly reduced its affinity for Pd(II), but the combination of porphyrin 1 and Pd(II) gave an ionophoric species that increased the rate of 5/6-carboxyfluorescein (5/6-CF) transit through the phospholipid bilayer 12-fold. A maximum in the 5/6-CF release rate was observed at a Pd(II) concentration of 4 μM, and the application of a solution-phase binding model to the membrane phase showed that this peak in ionophoric activity corresponded to the greatest extent of porphyrin oligomerization. Further studies suggested these Pd(II)/porphyrin oligomers transported 5/6-CF via a channel mechanism.
Collapse
Affiliation(s)
- Usha Devi
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | | | | | | |
Collapse
|
3
|
You L, Li R, Gokel GW. Anion transport properties of amine and amide-sidechained peptides are affected by charge and phospholipid composition. Org Biomol Chem 2008; 6:2914-23. [PMID: 18688484 PMCID: PMC3124115 DOI: 10.1039/b800530c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four synthetic anion transporters (SATs) having the general formula (n-C(18)H(37))(2)N-COCH(2)OCH(2)CO-(Gly)(3)Pro-Lys(epsilon-N-R)-(Gly)(2)-O-n-C(7)H(15) were prepared and studied. The group R was Cbz, H (TFA salt), t-Boc, and dansyl in peptides 1, 2, 3, and 4 respectively. The glutamine analog (GGGPQAG sequence) was also included. A dansyl-substituted fluorescent SAT was used to probe peptide insertion; the dansyl sidechain resides in an environment near the bilayer's midpolar regime. When the lysine sidechain was free or protected amine, little effect was noted on final Cl(-) transport rate in DOPC : DOPA (7 : 3) liposomes. This stands in contrast to the significant retardation of transport previously observed when a negative glutamate residue was present in the peptide sequence. It was also found that Cl(-) release from liposomes depended on the phospholipid composition of the vesicles. Chloride transport diminished significantly for the free lysine containing SAT, 2, when the lipid was altered from DOPC : DOPA to pure DOPC. Amide-sidechained SATs 1 and 5 showed a relatively small decrease in Cl(-) transport. The effect of lipid composition on Cl(-) transport was explained by differences in electrostatic interaction between amino acid sidechain and lipid headgroup, which was modeled by computation.
Collapse
Affiliation(s)
- Lei You
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Ruiqiong Li
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - George W. Gokel
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
- Departments of Chemistry & Biochemistry and Biology, Center for Nanoscience, University of Missouri-Saint Louis, One University Boulevard, Saint Louis, MO 63121, USA
| |
Collapse
|
4
|
Dopico AM, Tigyi GJ. A glance at the structural and functional diversity of membrane lipids. Methods Mol Biol 2007; 400:1-13. [PMID: 17951723 DOI: 10.1007/978-1-59745-519-0_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
In the postgenomic era, spatially and temporally regulated molecular interactions as signals are beginning to take center stage in the understanding of fundamental biological events. For years, reductionism derived from the "fluid mosaic" model of the cell membrane has portrayed membrane lipids as rather passive molecules that, whereas separating biologically relevant aqueous phases, provided an environment so that membrane proteins could fulfill the specificity and selectivity required for proper cell signaling. Whereas these roles for membrane lipids still stand, the structural diversity of lipids and their complex arrangement in supramolecular assemblies have expanded such limited, although fundamental roles. Growing developments in the field of membrane lipids help to understand biological phenomena at the nanoscale domain, and reveal this heterogeneous group of organic compounds as a long underestimated group of key regulatory molecules. In this introductory chapter, brief overviews of the structural diversity of membrane lipids, the impact of different lipids on membrane properties, the vertical organization of lipids into rafts and caveolae, and the functional role of lipids as mediators of inter- and intracellular signals are provided. Any comprehensive review on membrane lipids, whether emphasizing structural or functional aspects, will require several volumes. The purpose of this chapter is to provide both introduction and rationale for the selection of topics that lie ahead in this book. For this reason, the list of references primarily includes reviews on particular issues dealing with membrane lipids wherein the reader can find further references.
Collapse
Affiliation(s)
- Alex M Dopico
- Department of Pharmacology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | | |
Collapse
|
5
|
Kosinsky YA, Dubovskii PV, Nolde DE, Arseniev AS, Efremov RG. Fusion Peptide Interaction with Lipid Bilayer: Modeling with Monte Carlo Simulation and Continuum Electrostatics Calculation. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020008022380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
6
|
Efremov RG, Nolde DE, Volynsky PE, Arseniev AS. Modeling of Peptides in Implicit Membrane-Mimetic Media. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020008022376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
7
|
Haubertin DY, Madaoui H, Sanson A, Guérois R, Orlowski S. Molecular dynamics simulations of E. coli MsbA transmembrane domain: formation of a semipore structure. Biophys J 2006; 91:2517-31. [PMID: 16782794 PMCID: PMC1562368 DOI: 10.1529/biophysj.106.084020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human P-glycoprotein (MDR1/P-gp) is an ATP-binding cassette (ABC) transporter involved in cellular response to chemical stress and failures of anticancer chemotherapy. In the absence of a high-resolution structure for P-gp, we were interested in the closest P-gp homolog for which a crystal structure is available: the bacterial ABC transporter MsbA. Here we present the molecular dynamics simulations performed on the transmembrane domain of the open-state MsbA in a bilayer composed of palmitoyl oleoyl phosphatidylethanolamine lipids. The system studied contained more than 90,000 atoms and was simulated for 50 ns. This simulation shows that the open-state structure of MsbA can be stable in a membrane environment and provides invaluable insights into the structural relationships between the protein and its surrounding lipids. This study reveals the formation of a semipore-like structure stabilized by two key phospholipids which interact with the hinge region of the protein during the entire simulation. Multiple sequence alignments of ABC transporters reveal that one of the residues involved in the interaction with these two phospholipids are under a strong selection pressure specifically applied on the bacterial homologs of MsbA. Hence, comparison of molecular dynamics simulation and phylogenetic data appears as a powerful approach to investigate the functional relevance of molecular events occurring during simulations.
Collapse
Affiliation(s)
- David Y Haubertin
- Service de Biophysique des Fonctions Membranaires, Département de Biologie Joliot-Curie and URA 2096 CNRS, Direction des Sciences du Vivant/Commissariat á l'Energie Atomique (CEA), Centre de Saclay, 91191 Gif-sur-Yvette cedex, France
| | | | | | | | | |
Collapse
|
8
|
Banke TG, Dravid SM, Traynelis SF. Protons trap NR1/NR2B NMDA receptors in a nonconducting state. J Neurosci 2005; 25:42-51. [PMID: 15634765 PMCID: PMC6725198 DOI: 10.1523/jneurosci.3154-04.2005] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 11/13/2004] [Accepted: 11/14/2004] [Indexed: 11/21/2022] Open
Abstract
NMDA receptors are highly expressed in the CNS and are involved in excitatory synaptic transmission, as well as synaptic plasticity. Given that overstimulation of NMDA receptors can cause cell death, it is not surprising that these channels are under tight control by a series of inhibitory extracellular ions, including zinc, magnesium, and H+. We studied the inhibition by extracellular protons of recombinant NMDA receptor NR1/NR2B single-channel and macroscopic responses in transiently transfected human embryonic kidney HEK 293 cells using patch-clamp techniques. We report that proton inhibition proceeds identically in the absence or presence of agonist, which rules out the possibility that protonation inhibits receptors by altering coagonist binding. The response of macroscopic currents in excised patches to rapid jumps in pH was used to estimate the microscopic association and dissociation rates for protons, which were 1.4 x 10(9) m(-1) sec(-1) and 110-196 sec(-1), respectively (K(d) corresponds to pH 7.2). Protons reduce the open probability without altering the time course of desensitization or deactivation. Protons appear to slow at least one time constant describing the intra-activation shut-time histogram and modestly reduce channel open time, which we interpret to reflect a reduction in the overall channel activation rate and possible proton-induced termination of openings. This is consistent with a modest proton-dependent slowing of the macroscopic response rise time. From these data, we propose a physical model of proton inhibition that can describe macroscopic and single-channel properties of NMDA receptor function over a range of pH values.
Collapse
Affiliation(s)
- Tue G Banke
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | | | | |
Collapse
|
9
|
Bostick D, Berkowitz ML. The implementation of slab geometry for membrane-channel molecular dynamics simulations. Biophys J 2003; 85:97-107. [PMID: 12829468 PMCID: PMC1303069 DOI: 10.1016/s0006-3495(03)74458-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Slab geometric boundary conditions are applied in the molecular dynamics simulation of a simple membrane-channel system. The results of the simulation were compared to those of an analogous system using normal three-dimensional periodic boundary conditions. Analysis of the dynamics and electrostatics of the system show that slab geometric periodicity eliminates the artificial bulk water orientational polarization that is present while using normal three-dimensional periodicity. Furthermore, even though the water occupancy and volume of our simple channel is the same when using either method, the electrostatic properties are considerably different when using slab geometry. In particular, the orientational polarization of water is seen to be different in the interior of the channel. This gives rise to a markedly different electric field within the channel. We discuss the implications of slab geometry for the future simulation of this type of system and for the study of channel transport properties.
Collapse
Affiliation(s)
- David Bostick
- Department of Physics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | | |
Collapse
|
10
|
Affiliation(s)
- David J. Anick
- Harvard Medical School, McLean Hospital, Bowditch Building, 115 Mill St., Belmont, Massachusetts 02478
| |
Collapse
|
11
|
Sutherland J, Arteca GA. Geometrical modelling of Ohmic conductance in ion channels. J Mol Graph Model 2002; 21:101-10. [PMID: 12398341 DOI: 10.1016/s1093-3263(02)00126-2] [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: 11/24/2022]
Abstract
In an Ohmic model, channel conductivity can be described in terms of the geometry of a conducting cable. The essential features of such devices are the arc length of the curve describing the channel's longitudinal path, and the cross-sectional areas transversal to this curve. In a first approximation, conducting channels can be represented by an average molecular shape with estimated lengths and cross-sectional areas. Whereas the physical shortcomings of this approach are known, its accuracy limitations in practice have not been established. In this work, we discuss an improved model for the channel's shape, one that allows us to gauge how much of the Ohmic conductivity can be assigned purely to geometrical features. In the present algorithm, we investigate all regions inside the pore that are accessible to ions using various choices for the molecular surface of the inner channel. We discuss the agreement with experimental conductances in the case of 12 channels (cholera toxin B-subunit pentamer, Staphylococcus aureus alpha-hemolysin, Streptomyces lividans KcsA channel, seven porins, gramicidin A, and phospholamban). Our results can be regarded as a benchmark for the best performance that can be expected from a geometrical model of conductance. Consequently, significant deviations from experimental trends can safely be assigned to non-geometrical factors, namely the specific composition of the ion channel and the detailed electrostatic interactions between the channel and a particular ion.
Collapse
Affiliation(s)
- Jeffrey Sutherland
- Département de chimie et biochimie, Laurentian University, Sudbury, Ontario, Canada
| | | |
Collapse
|
12
|
Lapinsh M, Prusis P, Lundstedt T, Wikberg JES. Proteochemometrics modeling of the interaction of amine G-protein coupled receptors with a diverse set of ligands. Mol Pharmacol 2002; 61:1465-75. [PMID: 12021408 DOI: 10.1124/mol.61.6.1465] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have evaluated the proteochemometrics approach in the analysis of the interactions of a diverse set or organic ligands with subtypes of serotonin, dopamine, histamine, and adrenergic receptors. As used herein, proteochemometrics exploits affinity data for series of organic amines binding to wild-type amine G protein-coupled receptors, correlating it to descriptions and cross-description derived from the primary amino acid sequences of the receptors and the computed structures of the organic compounds. We show that after appropriate data preprocessing, statistically valid models that have good external predictive ability can be created. Evaluation of the models gave important quantitative insight into the mode of interactions of the amine G protein-coupled receptors with their ligands.
Collapse
Affiliation(s)
- Maris Lapinsh
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | | | | | | |
Collapse
|
13
|
Choma CT, Tieleman DP, Cregut D, Serrano L, Berendsen HJ. Towards the design and computational characterization of a membrane protein. J Mol Graph Model 2002; 20:219-34. [PMID: 11766047 DOI: 10.1016/s1093-3263(01)00111-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The design of a transmembrane four-helix bundle is described. We start with an idealized four-helix bundle geometry, then use statistical information to build a plausible transmembrane bundle. Appropriate residues are chosen using database knowledge on the sequences of membrane helices and loops, then the packing of the bundle core is optimized, and favorable side chain rotamers from rotamer libraries are selected. Next, we use explicit physical knowledge from biomolecular simulation force fields and molecular dynamics simulations to test whether the designed structure is physically possible. These procedures test whether the designed protein will indeed be alpha-helical, well packed and stable over a time scale of several nanoseconds in a realistic lipid bilayer environment. We then test a modeling approach that does not include sophisticated database knowledge about proteins, but rather relies on applying our knowledge of the physics that governs protein motions. This independent validation of the design is based on simulated annealing and restrained molecular dynamics simulation in vacuo, comparable to procedures used to refine NMR and X-ray structures.
Collapse
Affiliation(s)
- C T Choma
- Cogswell Lab, Department of Chemistry, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, USA.
| | | | | | | | | |
Collapse
|
14
|
Shenkarev ZO, Balashova TA, Efremov RG, Yakimenko ZA, Ovchinnikova TV, Raap J, Arseniev AS. Spatial structure of zervamicin IIB bound to DPC micelles: implications for voltage-gating. Biophys J 2002; 82:762-71. [PMID: 11806918 PMCID: PMC1301885 DOI: 10.1016/s0006-3495(02)75438-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Zervamicin IIB is a 16-amino acid peptaibol that forms voltage-dependent ion channels with multilevel conductance states in planar lipid bilayers and vesicular systems. The spatial structure of zervamicin IIB bound to dodecylphosphocholine micelles was studied by nuclear magnetic resonance spectroscopy. The set of 20 structures obtained has a bent helical conformation with a mean backbone root mean square deviation value of approximately 0.2 A and resembles the structure in isotropic solvents (Balashova et al., 2000. NMR structure of the channel-former zervamicin IIB in isotropic solvents. FEBS Lett 466:333-336). The N-terminus represents an alpha-helix, whereas the C-terminal part has a mixed 3(10)/alpha(R) hydrogen-bond pattern. In the anisotropic micelle environment, the bending angle on Hyp10 (23 degrees) is smaller than that (47 degrees) in isotropic solvents. In the NOESY (Nuclear Overhauser Effect Spectroscopy) spectra, the characteristic attenuation of the peptide signals by 5- and 16-doxylstearate relaxation probes indicates a peripheral mode of the peptaibol binding to the micelle with the N-terminus immersed slightly deeper into micelle interior. Analysis of the surface hydrophobicity reveals that the zervamicin IIB helix is amphiphilic and well suited to formation of a tetrameric transmembrane bundle, according to the barrel-stave mechanism. The results are discussed in a context of voltage-driven peptaibol insertion into membrane.
Collapse
Affiliation(s)
- Z O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | | | | | | | | | | | | |
Collapse
|
15
|
Kessel A, Ben-Tal N. Free energy determinants of peptide association with lipid bilayers. PEPTIDE-LIPID INTERACTIONS 2002. [DOI: 10.1016/s1063-5823(02)52010-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
16
|
Sompornpisut P, Liu YS, Perozo E. Calculation of rigid-body conformational changes using restraint-driven Cartesian transformations. Biophys J 2001; 81:2530-46. [PMID: 11606268 PMCID: PMC1301722 DOI: 10.1016/s0006-3495(01)75898-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We present an approach for calculating conformational changes in membrane proteins using limited distance information. The method, named restraint-driven Cartesian transformations, involves 1) the use of relative distance changes; 2) the systematic sampling of rigid body movements in Cartesian space; 3) a penalty evaluation; and 4) model refinement using energy minimization. As a test case, we have analyzed the structural basis of activation gating in the Streptomyces lividans potassium channel (KcsA). A total of 10 pairs of distance restraints derived from site-directed spin labeling and electron paramagnetic resonance (SDSL-EPR) spectra were used to calculate the open conformation of the second transmembrane domains of KcsA (TM2). The SDSL-EPR based structure reveals a gating mechanism consistent with a scissoring-type motion of the TM2 segments that includes a pivot point near middle of the helix. The present approach considerably reduces the amount of time and effort required to establish the overall nature of conformational changes in membrane proteins. It is expected that this approach can be implemented into restrained molecular dynamics protocol to calculate the structure and conformational changes in a variety of membrane protein systems.
Collapse
Affiliation(s)
- P Sompornpisut
- Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville, Virginia 22906-0011, USA
| | | | | |
Collapse
|
17
|
Fischer WB, Forrest LR, Smith GR, Sansom MS. Transmembrane domains of viral ion channel proteins: a molecular dynamics simulation study. Biopolymers 2000; 53:529-38. [PMID: 10766949 DOI: 10.1002/(sici)1097-0282(200006)53:7<529::aid-bip1>3.0.co;2-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanosecond molecular dynamics simulations in a fully solvated phospholipid bilayer have been performed on single transmembrane alpha-helices from three putative ion channel proteins encoded by viruses: NB (from influenza B), CM2 (from influenza C), and Vpu (from HIV-1). alpha-Helix stability is maintained within a core region of ca. 28 residues for each protein. Helix perturbations are due either to unfavorable interactions of hydrophobic residues with the lipid headgroups or to the need of the termini of short helices to extend into the surrounding interfacial environment in order to form H-bonds. The requirement of both ends of a helix to form favorable interactions with lipid headgroups and/or water may also lead to tilting and/or kinking of a transmembrane alpha-helix. Residues that are generally viewed as poor helix formers in aqueous solution (e.g., Gly, Ile, Val) do not destabilize helices, if located within a helix that spans a lipid bilayer. However, helix/bilayer mismatch such that a helix ends abruptly within the bilayer core destabilizes the end of the helix, especially in the presence of Gly and Ala residues. Hydrogen bonding of polar side-chains with the peptide backbone and with one another occurs when such residues are present within the bilayer core, thus minimizing the energetic cost of burying such side-chains.
Collapse
Affiliation(s)
- W B Fischer
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Rex Richards Building, South Parks Road, Oxford, OX1 3QU, UK.
| | | | | | | |
Collapse
|
18
|
Borisenko V, Sansom MS, Woolley GA. Protonation of lysine residues inverts cation/anion selectivity in a model channel. Biophys J 2000; 78:1335-48. [PMID: 10692320 PMCID: PMC1300733 DOI: 10.1016/s0006-3495(00)76688-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
A dimeric alamethicin analog with lysine at position 18 in the sequence (alm-K18) was previously shown to form stable anion-selective channels in membranes at pH 7.0 [Starostin, A. V., R. Butan, V. Borisenko, D. A. James, H. Wenschuh, M. S. Sansom, and G. A. Woolley. 1999. Biochemistry. 38:6144-6150]. To probe the charge state of the conducting channel and how this might influence cation versus anion selectivity, we performed a series of single-channel selectivity measurements at different pH values. At pH 7.0 and below, only anion-selective channels were found with P(K(+))/P(Cl(-)) = 0. 25. From pH 8-10, a mixture of anion-selective, non-selective, and cation-selective channels was found. At pH > 11 only cation-selective channels were found with P(K(+))/P(Cl(-)) = 4. In contrast, native alamethicin-Q18 channels (with Gln in place of Lys at position 18) were cation-selective (P(K(+))/P(Cl(-)) = 4) at all pH values. Continuum electrostatics calculations were then carried out using an octameric model of the alm-K18 channel embedded in a low dielectric slab to simulate a membrane. Although the calculations can account for the apparent pK(a) of the channel, they fail to correctly predict the degree of selectivity. Although a switch from cation- to anion-selectivity as the channel becomes protonated is indicated, the degree of anion-selectivity is severely overestimated, suggesting that the continuum approach does not adequately represent some aspect of the electrostatics of permeation in these channels. Side-chain conformational changes upon protonation, conformational changes, and deprotonation caused by permeating cations and counterion binding by lysine residues upon protonation are considered as possible sources of the overestimation.
Collapse
Affiliation(s)
- V Borisenko
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Canada
| | | | | |
Collapse
|
19
|
Kukol A, Arkin IT. Structure of the influenza C virus CM2 protein transmembrane domain obtained by site-specific infrared dichroism and global molecular dynamics searching. J Biol Chem 2000; 275:4225-9. [PMID: 10660588 DOI: 10.1074/jbc.275.6.4225] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 115-residue protein CM2 from Influenza C virus has been recently characterized as a tetrameric integral membrane glycoprotein. Infrared spectroscopy and site-directed infrared dichroism were utilized here to determine its transmembrane structure. The transmembrane domain of CM2 is alpha-helical, and the helices are tilted by beta = (14.6 +/- 3.0) degrees from the membrane normal. The rotational pitch angle about the helix axis omega for the 1-(13)C-labeled residues Gly(59) and Leu(66) is omega = (218 +/- 17) degrees, where omega is defined as zero for a residue pointing in the direction of the helix tilt. A detailed structure was obtained from a global molecular dynamics search utilizing the orientational data as an energy refinement term. The structure consists of a left-handed coiled-coil with a helix crossing angle of Omega = 16 degrees. The putative transmembrane pore is occluded by the residue Met(65). In addition hydrogen/deuterium exchange experiments show that the core is not accessible to water.
Collapse
Affiliation(s)
- A Kukol
- Cambridge Center for Molecular Recognition, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | | |
Collapse
|
20
|
Modeling of peptides and proteins in a membrane environment: I. A solvation model mimicking a lipid bilayer. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2000. [DOI: 10.1007/bf02759157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
21
|
Kessel A, Cafiso DS, Ben-Tal N. Continuum solvent model calculations of alamethicin-membrane interactions: thermodynamic aspects. Biophys J 2000; 78:571-83. [PMID: 10653772 PMCID: PMC1300662 DOI: 10.1016/s0006-3495(00)76617-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Alamethicin is a 20-amino acid antibiotic peptide that forms voltage-gated ion channels in lipid bilayers. Here we report calculations of its association free energy with membranes. The calculations take into account the various free-energy terms that contribute to the transfer of the peptide from the aqueous phase into bilayers of different widths. The electrostatic and nonpolar contributions to the solvation free energy are calculated using continuum solvent models. The contributions from the lipid perturbation and membrane deformation effects and the entropy loss associated with peptide immobilization in the bilayer are estimated from a statistical thermodynamic model. The calculations were carried out using two classes of experimentally observed conformations, both of which are helical: the NMR and the x-ray crystal structures. Our calculations show that alamethicin is unlikely to partition into bilayers in any of the NMR conformations because they have uncompensated backbone hydrogen bonds and their association with the membrane involves a large electrostatic solvation free energy penalty. In contrast, the x-ray conformations provide enough backbone hydrogen bonds for the peptide to associate with bilayers. We tested numerous transmembrane and surface orientations of the peptide in bilayers, and our calculations indicate that the most favorable orientation is transmembrane, where the peptide protrudes approximately 4 A into the water-membrane interface, in very good agreement with electron paramagnetic resonance and oriented circular dichroism measurements. The calculations were carried out using two alamethicin isoforms: one with glutamine and the other with glutamate in the 18th position. The calculations indicate that the two isoforms have similar membrane orientations and that their insertion into the membrane is likely to involve a 2-A deformation of the bilayer, again, in good agreement with experimental data. The implications of the results for the biological function of alamethicin and its capacity to oligomerize and form ion channels are discussed.
Collapse
Affiliation(s)
- A Kessel
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | | | | |
Collapse
|
22
|
Forrest LR, Kukol A, Arkin IT, Tieleman DP, Sansom MS. Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer. Biophys J 2000; 78:55-69. [PMID: 10620273 PMCID: PMC1300617 DOI: 10.1016/s0006-3495(00)76572-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The M2 protein of influenza A virus forms homotetrameric helix bundles, which function as proton-selective channels. The native form of the protein is 97 residues long, although peptides representing the transmembrane section display ion channel activity, which (like the native channel) is blocked by the antiviral drug amantadine. As a small ion channel, M2 may provide useful insights into more complex channel systems. Models of tetrameric bundles of helices containing either 18 or 22 residues have been simulated while embedded in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidylcholine bilayer. Several different starting models have been used. These suggest that the simulation results, at least on a nanosecond time scale, are sensitive to the exact starting structure. Electrostatics calculations carried out on a ring of four ionizable aspartate residues at the N-terminal mouth of the channel suggest that at any one time, only one will be in a charged state. Helix bundle models were mostly stable over the duration of the simulation, and their helices remained tilted relative to the bilayer normal. The M2 helix bundles form closed channels that undergo breathing motions, alternating between a tetramer and a dimer-of-dimers structure. Under these conditions either the channel forms a pocket of trapped waters or it contains a column of waters broken predominantly at the C-terminal mouth of the pore. These waters exhibit restricted motion in the pore and are effectively "frozen" in a way similar to those seen in previous simulations of a proton channel formed by a four-helix bundle of a synthetic leucine-serine peptide (, Biophys. J. 77:2400-2410).
Collapse
Affiliation(s)
- L R Forrest
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | | | | | | | | |
Collapse
|
23
|
Kukol A, Arkin IT. vpu transmembrane peptide structure obtained by site-specific fourier transform infrared dichroism and global molecular dynamics searching. Biophys J 1999; 77:1594-601. [PMID: 10465770 PMCID: PMC1300447 DOI: 10.1016/s0006-3495(99)77007-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The recently developed method of site-directed Fourier transform infrared dichroism for obtaining orientational constraints of oriented polymers is applied here to the transmembrane domain of the vpu protein from the human immunodeficiency virus type 1 (HIV-1). The infrared spectra of the 31-residue-long vpu peptide reconstituted in lipid vesicles reveal a predominantly alpha-helical structure. The infrared dichroism data of the (13)C-labeled peptide yielded a helix tilt beta = (6.5 +/- 1.7) degrees from the membrane normal. The rotational pitch angle omega, defined as zero for a residue located in the direction of the helix tilt, is omega = (283 +/- 11) degrees for the (13)C labels Val(13)/Val(20) and omega = (23 +/- 11) degrees for the (13)C labels Ala(14)/Val(21). A global molecular dynamics search protocol restraining the helix tilt to the experimental value was performed for oligomers of four, five, and six subunits. From 288 structures for each oligomer, a left-handed pentameric coiled coil was obtained, which best fits the experimental data. The structure reveals a pore occluded by Trp residues at the intracellular end of the transmembrane domain.
Collapse
Affiliation(s)
- A Kukol
- Cambridge Center for Molecular Recognition, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England
| | | |
Collapse
|
24
|
Pashkov VS, Maslennikov IV, Tchikin LD, Efremov RG, Ivanov VT, Arseniev AS. Spatial structure of the M2 transmembrane segment of the nicotinic acetylcholine receptor alpha-subunit. FEBS Lett 1999; 457:117-21. [PMID: 10486576 DOI: 10.1016/s0014-5793(99)01023-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A synthetic peptide corresponding to the transmembrane segment M2 (residues 236-267) of the alpha-subunit of the nicotinic acetylcholine receptor from Torpedo californica has been studied by two dimensional 1H-NMR spectroscopy in a chloroform-methanol (1:1) mixture containing 0.1 M LiClO4. Reconstruction of the spatial structure of M2 from the NMR data resulted in an alpha-helix formed by residues 241-263. Distribution of the molecular hydrophobicity potential on the helix surface is very similar to that in five-helix bundles of proteins with a known three dimensional structure: two hydrophilic bands located on the opposite helix sides separated by strong hydrophobic zones.
Collapse
Affiliation(s)
- V S Pashkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | | |
Collapse
|
25
|
Abstract
Membrane proteins, of which the majority seem to contain one or more alpha-helix, constitute approx. 30% of most genomes. A complete understanding of the nature of helix/bilayer interactions is necessary for an understanding of the structural principles underlying membrane proteins. This review describes computer simulation studies of helix/bilayer interactions. Key experimental studies of the interactions of alpha-helices and lipid bilayers are briefly reviewed. Surface associated helices are found in some membrane-bound enzymes (e.g. prostaglandin synthase), and as stages in the mechanisms of antimicrobial peptides and of pore-forming bacterial toxins. Transmembrane alpha-helices are found in most integral membrane proteins, and also in channels formed by amphipathic peptides or by bacterial toxins. Mean field simulations, in which the lipid bilayer is approximated as a hydrophobic continuum, have been used in studies of membrane-active peptides (e.g. alamethicin, melittin, magainin and dermaseptin) and of simple membrane proteins (e.g. phage Pf1 coat protein). All atom molecular dynamics simulations of fully solvated bilayers with transmembrane helices have been applied to: the constituent helices of bacteriorhodopsin; peptide-16 (a simple model TM helix); and a number of pore-lining helices from ion channels. Surface associated helices (e.g. melittin and dermaseptin) have been simulated, as have alpha-helical bundles such as bacteriorhodopsin and alamethicin. From comparison of the results from the two classes of simulation, it emerges that a major theoretical challenge is to exploit the results of all atom simulations in order to improve the mean field approach.
Collapse
Affiliation(s)
- P C Biggin
- Salk Institute for Biological Studies, La Jolla, CA 92109, USA
| | | |
Collapse
|
26
|
Abstract
In a number of membrane-bound viruses, ion channels are formed by integral membrane proteins. These channel proteins include M2 from influenza A, NB from influenza B, and, possibly, Vpu from HIV-1. M2 is important in facilitating uncoating of the influenza A viral genome and is the target of amantadine, an anti-influenza drug. The biological roles of NB and Vpu are less certain. In all cases, the protein contains a single transmembrane alpha-helix close to its N-terminus. Channels can be formed by homo-oligomerization of these proteins, yielding bundles of transmembrane helices that span the membrane and surround a central ion-permeable pore. Molecular modeling may be used to integrate and interpret available experimental data concerning the structure of such transmembrane pores. This has proved successful for the M2 channel domain, where two independently derived models are in agreement with one another, and with solid-state nuclear magnetic resonance (NMR) data. Simulations based on channel models may yield insights into possible ion conduction and selectivity mechanisms.
Collapse
Affiliation(s)
- M S Sansom
- Department of Biochemistry, University of Oxford, UK.
| | | | | |
Collapse
|