Molecular Insight into Affinities of Drugs and Their Metabolites to Lipid Bilayers

2013 ◽  
Vol 117 (8) ◽  
pp. 2403-2410 ◽  
Author(s):  
Markéta Paloncýová ◽  
Karel Berka ◽  
Michal Otyepka
Keyword(s):  
Lipid Bilayers ◽  
Insight Into

scholarly journals Channel noise in nerve membranes and lipid bilayers

1975 ◽  
Vol 8 (4) ◽  
pp. 451-506 ◽  
Author(s):  
F Conti ◽  
E. Wanke
Keyword(s):  
Brownian Motion ◽  
Lipid Bilayers ◽  
Fluctuation Phenomena ◽  
Channel Noise ◽  
Fluctuation Analysis ◽  
Electronic Charge ◽  
Basic Principles ◽  
Avogadro’S Number ◽  
Insight Into

The basic principles underlying fluctuation phenomena in thermodynamics have long been understood (for reviews see Kubo, 1957; Kubo, Matsuo & Kazuhiro 1973 Lax, 1960). Classical examples of how fluctuation analysis can provide an insight into the corpuscular nature of matter are the determination of Avogadro's number according to Einstein's theory of Brownian motion (see, e.g. Uhlenbeck & Ornstein, 1930; Kac, 1947) and the evaluation of the electronic charge from the shot noise in vacuum tubes (see Van der Ziel, 1970).

scholarly journals Cryo-EM structures of the DCPIB-inhibited volume-regulated anion channel LRRC8A in lipid nanodiscs

2018 ◽  
Author(s):  
David M. Kern ◽  
SeCheol Oh ◽  
Richard K. Hite ◽  
Stephen G. Brohawn
Keyword(s):  
Lipid Bilayers ◽  
Critical Role ◽  
Anion Channel ◽  
Lipid Binding ◽  
Channel Structure ◽  
Anion Channels ◽  
Cryo Electron Microscopy ◽  
Lipid Nanodiscs ◽  
Insight Into

AbstractHypoosmotic conditions activate volume-regulated anion channels in vertebrate cells. These channels are formed by leucine-rich repeat-containing protein 8 (LRRC8) family members and contain LRRC8A in homo- or hetero-hexameric assemblies. Here we present single-particle cryo-electron microscopy structures of LRRC8A in complex with the inhibitor DCPIB reconstituted in lipid nanodiscs. DCPIB plugs the channel like a cork in a bottle - binding in the extracellular selectivity filter and sterically occluding ion conduction. Constricted and expanded structures reveal coupled dilation of cytoplasmic LRRs and the channel pore, suggesting a mechanism for channel gating by internal stimuli. Conformational and symmetry differences between LRRC8A structures determined in detergent micelles and lipid bilayers related to reorganization of intersubunit lipid binding sites demonstrate a critical role for the membrane in determining channel structure. These results provide insight into LRRC8 gating and inhibition and the role of lipids in the structure of an ionic-strength sensing ion channel.

scholarly journals Palmitoylated Cysteines in Chikungunya Virus nsP1 Are Critical for Targeting to Cholesterol-Rich Plasma Membrane Microdomains with Functional Consequences for Viral Genome Replication

2020 ◽  
Vol 94 (10) ◽  
Author(s):  
William Bakhache ◽  
Aymeric Neyret ◽  
Eric Bernard ◽  
Andres Merits ◽  
Laurence Briant
Keyword(s):  
Plasma Membrane ◽  
Lipid Bilayers ◽  
Functional Role ◽  
Membrane Microdomains ◽  
Genome Replication ◽  
Functional Importance ◽  
Late Endosomes ◽  
Plasma Membrane Microdomains ◽  
Insight Into

ABSTRACT In mammalian cells, alphavirus replication complexes are anchored to the plasma membrane. This interaction with lipid bilayers is mediated through the viral methyl/guanylyltransferase nsP1 and reinforced by palmitoylation of cysteine residue(s) in the C-terminal region of this protein. Lipid content of membranes supporting nsP1 anchoring remains poorly studied. Here, we explore the membrane binding capacity of nsP1 with regard to cholesterol. Using the medically important chikungunya virus (CHIKV) as a model, we report that nsP1 cosegregates with cholesterol-rich detergent-resistant membrane microdomains (DRMs), also called lipid rafts. In search for the critical factor for cholesterol partitioning, we identify nsP1 palmitoylated cysteines as major players in this process. In cells infected with CHIKV or transfected with CHIKV trans-replicase plasmids, nsP1, together with the other nonstructural proteins, are detected in DRMs. While the functional importance of CHIKV nsP1 preference for cholesterol-rich membrane domains remains to be determined, we observed that U18666A- and imipramine-induced sequestration of cholesterol in late endosomes redirected nsP1 to these compartments and simultaneously dramatically decreased CHIKV genome replication. A parallel study of Sindbis virus (SINV) revealed that nsP1 from this divergent alphavirus displays a low affinity for cholesterol and only moderately segregates with DRMs. Behaviors of CHIKV and SINV with regard to cholesterol, therefore, match with the previously reported differences in the requirement for nsP1 palmitoylation, which is dispensable for SINV but strictly required for CHIKV replication. Altogether, this study highlights the functional importance of nsP1 segregation with DRMs and provides new insight into the functional role of nsP1 palmitoylated cysteines during alphavirus replication. IMPORTANCE Functional alphavirus replication complexes are anchored to the host cell membranes through the interaction of nsP1 with the lipid bilayers. In this work, we investigate the importance of cholesterol for such an association. We show that nsP1 has affinity for cholesterol-rich membrane microdomains formed at the plasma membrane and identify conserved palmitoylated cysteine(s) in nsP1 as the key determinant for cholesterol affinity. We demonstrate that drug-induced cholesterol sequestration in late endosomes not only redirects nsP1 to this compartment but also dramatically decreases genome replication, suggesting the functional importance of nsP1 targeting to cholesterol-rich plasma membrane microdomains. Finally, we show evidence that nsP1 from chikungunya and Sindbis viruses displays different sensitivity to cholesterol sequestering agents that parallel with their difference in the requirement for nsP1 palmitoylation for replication. This research, therefore, gives new insight into the functional role of palmitoylated cysteines in nsP1 for the assembly of functional alphavirus replication complexes in their mammalian host.

New insight into probe-location dependent polarity and hydration at lipid/water interfaces: comparison between gel- and fluid-phases of lipid bilayers

2016 ◽  
Vol 18 (35) ◽  
pp. 24185-24197 ◽  
Author(s):  
Moirangthem Kiran Singh ◽  
Him Shweta ◽  
Mohammad Firoz Khan ◽  
Sobhan Sen
Keyword(s):  
Lipid Bilayers ◽  
Fluid Phase ◽  
Probe Location ◽  
Fluorescent Molecules ◽  
Insight Into ◽  
Fluid Phases

Location dependent polarity and hydration probed by a new series of 4-aminophthalimide-based fluorescent molecules (4AP-Cn;n= 2–10, 12) show different behaviour at gel- and fluid-phase lipid/water interfaces.

scholarly journals Structural and Functional Analysis of the Pore-Forming Toxin NetB from Clostridium perfringens

mBio ◽  
2013 ◽  
Vol 4 (1) ◽  
Author(s):  
Xu-Xia Yan ◽  
Corrine J. Porter ◽  
Simon P. Hardy ◽  
David Steer ◽  
A. Ian Smith ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Clostridium Perfringens ◽  
Pore Formation ◽  
Random Mutagenesis ◽  
Planar Lipid Bilayers ◽  
Necrotic Enteritis ◽  
Channel Conductance ◽  
Content Type ◽  
Alpha Hemolysin ◽  
Insight Into

ABSTRACT Clostridium perfringens is an anaerobic bacterium that causes numerous important human and animal diseases, primarily as a result of its ability to produce many different protein toxins. In chickens, C. perfringens causes necrotic enteritis, a disease of economic importance to the worldwide poultry industry. The secreted pore-forming toxin NetB is a key virulence factor in the pathogenesis of avian necrotic enteritis and is similar to alpha-hemolysin, a β-barrel pore-forming toxin from Staphylococcus aureus. To address the molecular mechanisms underlying NetB-mediated tissue damage, we determined the crystal structure of the monomeric form of NetB to 1.8 Å. Structural comparisons with other members of the alpha-hemolysin family revealed significant differences in the conformation of the membrane binding domain. These data suggested that NetB may recognize different membrane receptors or use a different mechanism for membrane-protein interactions. Consistent with this idea, electrophysiological experiments with planar lipid bilayers revealed that NetB formed pores with much larger single-channel conductance than alpha-hemolysin. Channel conductance varied with phospholipid net charge. Furthermore, NetB differed in its ion selectivity, preferring cations over anions. Using hemolysis as a screen, we carried out a random-mutagenesis study that identified several residues that are critical for NetB-induced cell lysis. Mapping of these residues onto the crystal structure revealed that they were clustered in regions predicted to be required for oligomerization or membrane binding. Together these data provide an insight into the mechanism of NetB-mediated pore formation and will contribute to our understanding of the mode of action of this important toxin. IMPORTANCE Necrotic enteritis is an economically important disease of the worldwide poultry industry and is mediated by Clostridium perfringens strains that produce NetB, a β-pore-forming toxin. We carried out structural and functional studies of NetB to provide a mechanistic insight into its mode of action and to assist in the development of a necrotic enteritis vaccine. We determined the structure of the monomeric form of NetB to 1.8 Å, used both site-directed and random mutagenesis to identify key residues that are required for its biological activity, and analyzed pore formation by NetB and its substitution-containing derivatives in planar lipid bilayers.

scholarly journals Organization of Model Helical Peptides in Lipid Bilayers: Insight into the Behavior of Single-Span Protein Transmembrane Domains

2002 ◽  
Vol 83 (1) ◽  
pp. 345-358 ◽  
Author(s):  
Simon Sharpe ◽  
Kathryn R. Barber ◽  
Chris W.M. Grant ◽  
David Goodyear ◽  
Michael R. Morrow
Keyword(s):  
Lipid Bilayers ◽  
Transmembrane Domains ◽  
Helical Peptides ◽  
Insight Into

scholarly journals Generation of high curvature membranes mediated by direct endophilin bilayer interactions

2001 ◽  
Vol 155 (2) ◽  
pp. 193-200 ◽  
Author(s):  
Khashayar Farsad ◽  
Niels Ringstad ◽  
Kohji Takei ◽  
Scott R. Floyd ◽  
Kristin Rose ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Membrane Trafficking ◽  
Potential Role ◽  
Transferase Activity ◽  
Endocytic Vesicle ◽  
Vesicle Budding ◽  
Amino Acid Stretch ◽  
Lipid Tubules ◽  
Insight Into

Endophilin 1 is a presynaptically enriched protein which binds the GTPase dynamin and the polyphosphoinositide phosphatase synptojanin. Perturbation of endophilin function in cell-free systems and in a living synapse has implicated endophilin in endocytic vesicle budding (Ringstad, N., H. Gad, P. Low, G. Di Paolo, L. Brodin, O. Shupliakov, and P. De Camilli. 1999. Neuron. 24:143–154; Schmidt, A., M. Wolde, C. Thiele, W. Fest, H. Kratzin, A.V. Podtelejnikov, W. Witke, W.B. Huttner, and H.D. Soling. 1999. Nature. 401:133–141; Gad, H., N. Ringstad, P. Low, O. Kjaerulff, J. Gustafsson, M. Wenk, G. Di Paolo, Y. Nemoto, J. Crun, M.H. Ellisman, et al. 2000. Neuron. 27:301–312). Here, we show that purified endophilin can directly bind and evaginate lipid bilayers into narrow tubules similar in diameter to the neck of a clathrin-coated bud, providing new insight into the mechanisms through which endophilin may participate in membrane deformation and vesicle budding. This property of endophilin is independent of its putative lysophosphatydic acid acyl transferase activity, is mediated by its NH2-terminal region, and requires an amino acid stretch homologous to a corresponding region in amphiphysin, a protein previously shown to have similar effects on lipid bilayers (Takei, K., V.I. Slepnev, V. Haucke, and P. De Camilli. 1999. Nat. Cell Biol. 1:33–39). Endophilin cooligomerizes with dynamin rings on lipid tubules and inhibits dynamin's GTP-dependent vesiculating activity. Endophilin B, a protein with homology to endophilin 1, partially localizes to the Golgi complex and also deforms lipid bilayers into tubules, underscoring a potential role of endophilin family members in diverse tubulovesicular membrane-trafficking events in the cell.

Cyclic phosphate-linked oligosaccharides (CyPLOS): Novel carbohydrate-based synthetic ion transporters

2011 ◽  
Vol 84 (1) ◽  
pp. 87-96
Author(s):  
Daniela Montesarchio
Keyword(s):  
Lipid Bilayers ◽  
Fine Tuning ◽  
Tetraethylene Glycol ◽  
Ion Transporters ◽  
Naturally Occurring ◽  
Spin Resonance ◽  
Conformational Properties ◽  
Cyclic Phosphate ◽  
Fluorescent Tag ◽  
Insight Into

Artificial ion transporters are synthetic molecules mimicking at a functional level the activity of naturally occurring ion channels or carriers. In the frame of cyclodextrin mimicry, we recently described the synthesis and conformational properties of new carbohydrate-based macrocycles having the glucoside units connected through 4,6-linked phosphodiester linkages, named CyPLOS (cyclic phosphate-linked oligosaccharides). The cyclic dimer was then adopted as a versatile synthetic platform to obtain a variety of analogs, carrying long linear alkyl or polyether chains. Diverse, jellyfish-shaped amphiphilic CyPLOS were thus obtained, with the compound carrying four tetraethylene glycol (TEG) tentacles acting as good ion transporter through lipid bilayers. A fine tuning of the properties and complexation abilities of these amphiphilic analogs was realized by introducing special reporter groups at the extremities of the TEG tentacles. Through the design of an azido-TEG functionalized key intermediate, a fluorescently labeled CyPLOS derivative was synthesized, showing a markedly increased ionophore activity, with the fluorescent tag also allowing the investigation of its mechanism of action and localization within the phospholipid bilayers. Incorporation of a spin label at the CyPLOS tentacles—to provide further insight into the study of their interactions with phospholipid membranes by electron spin resonance (ESR) spectroscopy—was also profitably achieved through a postsynthetic functionalization approach.

Wrapping and Internalization of Nanoparticles by Lipid Bilayers: a Computer Simulation Study

2011 ◽  
Vol 64 (7) ◽  
pp. 894 ◽  
Author(s):  
Kai Yang ◽  
Yu-qiang Ma
Keyword(s):  
Lipid Bilayers ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Lipid Vesicle ◽  
Adhesive Interaction ◽  
Computer Simulation Study ◽  
Lipid Domain ◽  
Internalization Process ◽  
Insight Into ◽  
Particle Internalization

Endocytosis is a basic pathway for nanoparticles to enter or leave cells. However, because of the complexity of the cell membrane, the mechanism of endocytosis is largely elusive. By dissipative particle dynamics (DPD), we investigate the wrapping and internalization processes of different particles (e.g., spheres and ellipsoids) by a lipid vesicle. It is found that rotation is possibly an important mechanism in the particle internalization process under a strong adhesive interaction, which can adjust the configuration of the nanoparticle to the lipid bilayer and facilitate the progress of the wrapping. Furthermore, the fission behaviour of the vesicle and the wrapped particle is also observed when the lipid domain is considered in the system. These simulation results give an insight into the nature of endocytosis.

scholarly journals Structure and dynamics of the drug-bound bacterial transporter EmrE in lipid bilayers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alexander A. Shcherbakov ◽  
Grant Hisao ◽  
Venkata S. Mandala ◽  
Nathan E. Thomas ◽  
Mohammad Soltani ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Solid State Nmr ◽  
Drug Binding ◽  
Future Design ◽  
Structure And Dynamics ◽  
Binding Residue ◽  
Drug Binding Site ◽  
Subunit B ◽  
Experimental Structure ◽  
Insight Into

AbstractThe dimeric transporter, EmrE, effluxes polyaromatic cationic drugs in a proton-coupled manner to confer multidrug resistance in bacteria. Although the protein is known to adopt an antiparallel asymmetric topology, its high-resolution drug-bound structure is so far unknown, limiting our understanding of the molecular basis of promiscuous transport. Here we report an experimental structure of drug-bound EmrE in phospholipid bilayers, determined using 19F and 1H solid-state NMR and a fluorinated substrate, tetra(4-fluorophenyl) phosphonium (F4-TPP+). The drug-binding site, constrained by 214 protein-substrate distances, is dominated by aromatic residues such as W63 and Y60, but is sufficiently spacious for the tetrahedral drug to reorient at physiological temperature. F4-TPP+ lies closer to the proton-binding residue E14 in subunit A than in subunit B, explaining the asymmetric protonation of the protein. The structure gives insight into the molecular mechanism of multidrug recognition by EmrE and establishes the basis for future design of substrate inhibitors to combat antibiotic resistance.

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