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Journal of Membrane Biology

Konstantina Karathanou, Ana-Nicoleta Bondar
Lipid membrane interfaces are complex environments that host essential cellular processes such as binding of proteins or drug molecules. A key open question is how water molecules at the interface of membranes with anionic lipids participate in protein binding. To address this question, we studied the dynamics of water hydrogen bonding at the interface of membranes composed of phosphatidylcholine and phosphatidylglycerol, and implemented an algorithm to identify hydrogen-bonded networks at the interface of a lipid membrane, and to characterize their dynamics and linear connections...
March 9, 2018: Journal of Membrane Biology
James C Gumbart, Martin B Ulmschneider, Anthony Hazel, Stephen H White, Jakob P Ulmschneider
We show that the free energy of inserting hydrophobic peptides into lipid bilayer membranes from surface-aligned to transmembrane inserted states can be reliably calculated using atomistic models. We use two entirely different computational methods: high temperature spontaneous peptide insertion calculations as well as umbrella sampling potential-of-mean-force (PMF) calculations, both yielding the same energetic profiles. The insertion free energies were calculated using two different protein and lipid force fields (OPLS protein/united-atom lipids and CHARMM36 protein/all-atom lipids) and found to be independent of the simulation parameters...
March 8, 2018: Journal of Membrane Biology
Nadia Elghobashi-Meinhardt, Prasad Phatak, Ana-Nicoleta Bondar, Marcus Elstner, Jeremy C Smith
For the photocycle of the membrane protein bacteriorhodopsin to proceed efficiently, the thermal 13-cis to all-trans back-isomerization of the retinal chromophore must return the protein to its resting state on a time-scale of milliseconds. Here, we report on quantum mechanical/molecular mechanical energy calculations examining the structural and energetic determinants of the retinal cis-trans isomerization in the protein environment. The results suggest that a hydrogen-bonded network consisting of the retinal Schiff base, active site amino acid residues, and water molecules can stabilize the twisted retinal, thus reducing the intrinsic energy cost of the cis-trans thermal isomerization barrier...
March 8, 2018: Journal of Membrane Biology
Małgorzata Jurak, Robert Mroczka, Rafał Łopucki
Lauryl gallate (LG) is an antioxidant agent. However, it exhibits poor solubility in water. Its interactions with the membrane result in structure evolution thus affecting the membrane functionality. In this paper the Brewster angle microscope coupled with the Langmuir trough was applied to determine the morphology, phase behaviour, thickness and miscibility of ternary Langmuir monolayers with equal mole fractions of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC); 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and an increasing mole fraction of LG...
March 7, 2018: Journal of Membrane Biology
Anne Grethen, David Glueck, Sandro Keller
Styrene/maleic acid (SMA) and related copolymers are attracting great interest because they solubilise membrane proteins and lipids to form polymer-encapsulated nanodiscs. These nanodiscs retain a lipid-bilayer core surrounded by a polymer rim and can harbour a membrane protein or a membrane-protein complex. SMA exists in different styrene/maleic acid molar ratios, which results in differences in hydrophobicity and solubilisation properties. We have recently demonstrated fast collisional lipid transfer among nanodiscs encapsulated by the relatively hydrophobic copolymer SMA(3:1)...
March 5, 2018: Journal of Membrane Biology
Saša Rezelj, Mirijam Kozorog, Tomaž Švigelj, Nataša Poklar Ulrih, Nada Žnidaršič, Marjetka Podobnik, Gregor Anderluh
Archaeosomes are vesicles made of lipids from archaea. They possess many unique features in comparison to other lipid systems, with their high stability being the most prominent one, making them a promising system for biotechnological applications. Here, we report a preparation protocol of large unilamellar vesicles, giant unilamellar vesicles (GUVs), and nanodiscs from archaeal lipids with incorporated cholesterol. Incorporation of cholesterol led to additional increase in thermal stability of vesicles. Surface plasmon resonance, sedimentation assays, intrinsic tryptophan fluorescence measurements, calcein release experiments, and GUVs experiments showed that members of cholesterol-dependent cytolysins, listeriolysin O (LLO), and perfringolysin O (PFO), bind to cholesterol-rich archaeosomes and thereby retain their pore-forming activity...
February 23, 2018: Journal of Membrane Biology
Alma E V Andersson, Marina A Kasimova, Lucie Delemotte
Viral potassium channels (Kcv) are homologous to the pore module of complex [Formula: see text]-selective ion channels of cellular organisms. Due to their relative simplicity, they have attracted interest towards understanding the principles of [Formula: see text] conduction and channel gating. In this work, we construct a homology model of the [Formula: see text] open state, which we validate by studying the binding of known blockers and by monitoring ion conduction through the channel. Molecular dynamics simulations of this model reveal that the re-orientation of selectivity filter carbonyl groups coincides with the transport of potassium ions, suggesting a possible mechanism for fast gating...
February 23, 2018: Journal of Membrane Biology
Yu-Di Hsu, Yu-Fen Huang, Yih-Jiuan Pan, Li-Kun Huang, Ya-Yun Liao, Wei-Hua Lin, Tzu-Yin Liu, Ching-Hung Lee, Rong-Long Pan
Plant vacuolar H + -transporting inorganic pyrophosphatase (V-PPase; EC is a crucial enzyme that exists on the tonoplast to maintain pH homeostasis across the vacuolar membrane. This enzyme generates proton gradient between cytosol and vacuolar lumen by hydrolysis of a metabolic byproduct, pyrophosphate (PP i ). The regulation of V-PPase at protein level has drawn attentions of many workers for decades, but its mechanism is still unclear. In this work, we show that AVP1, the V-PPase from Arabidopsis thaliana, is a target protein for regulatory 14-3-3 proteins at the vacuolar membrane, and all twelve 14-3-3 isoforms were analyzed for their association with AVP1...
February 16, 2018: Journal of Membrane Biology
Kangmin Duan, Ayush Kumar
No abstract text is available yet for this article.
February 14, 2018: Journal of Membrane Biology
Tahereh Ghane, Rene F Gorriz, Sandro Wrzalek, Senta Volkenandt, Ferand Dalatieh, Marco Reidelbach, Petra Imhof
Proton transfer in cytochrome c oxidase (CcO) from the cellular inside to the binuclear redox centre as well as proton pumping through the membrane takes place through proton entrance via two distinct pathways, the D- and K-channel. Both channels show a dependence of their hydration level on the protonation states of their key residues, K362 for the K-channel, and E286 or D132 for the D-channel. In the oxidative half of CcO's catalytic cycle the D-channel is the proton-conducting path. For this channel, an interplay of protonation state of the D-channel residues with the water and hydrogen-bond dynamics has been observed in molecular dynamics simulations of the CcO protein, embedded in a lipid bi-layer, modelled in different protonation states...
February 12, 2018: Journal of Membrane Biology
Desirée Magalhães Dos Santos, Camila Valesca Jardim Rocha, Elita Ferreira da Silveira, Marcelo Augusto Germani Marinho, Marisa Raquel Rodrigues, Nichole Osti Silva, Ailton da Silva Ferreira, Neusa Fernandes de Moura, Gabriel Jorge Sagrera Darelli, Elizandra Braganhol, Ana Paula Horn, Vânia Rodrigues de Lima
Rapanea ferruginea antioxidant and antitumoral properties were not explored before in literature. This study aimed to investigate these biological activities for the R. ferruginea leaf extract and correlate them with its phenolic content and influence in biological membrane dynamics. Thus, in this study, anti/pro-oxidative properties of R. ferruginea leaf extract by in vitro DPPH and TBARS assays, with respect to the free radical reducing potential and to its activity regarding membrane free radical-induced peroxidation, respectively...
February 8, 2018: Journal of Membrane Biology
Victoria Oakes, Carmen Domene
Cholesterol is a major constituent of the plasma membrane in higher order eukaryotes. The effect of cholesterol on the structure and organisation of cell membranes has been studied extensively by both experimental and computational means. In recent years, a wealth of data has been accumulated illustrating how subtle differences in the structure of cholesterol equate to considerable changes in the physical properties of the membrane. The effect of cholesterol stereoisomers, in particular, has been established, identifying a direct link with the activity of specific membrane proteins...
January 30, 2018: Journal of Membrane Biology
Ramazan Bal, Gurkan Ozturk, Ebru Onalan Etem, Aydin Him, Nurattin Cengiz, Tuncay Kuloglu, Mehmet Tuzcu, Caner Yildirim, Ahmet Tektemur
Major voltage-activated ionic channels of stellate cells in the ventral part of cochlear nucleus (CN) were largely characterized previously. However, it is not known if these cells are equipped with other ion channels apart from the voltage-sensitive ones. In the current study, it was aimed to study subunit composition and function of ATP-sensitive potassium channels (KATP) in stellate cells of the ventral cochlear nucleus. Subunits of KATP channels, Kir6.1, Kir6.2, SUR1, and SUR2, were expressed at the mRNA level and at the protein level in the mouse VCN tissue...
January 29, 2018: Journal of Membrane Biology
Bradley D Steiner, Allison R Eberly, Melanie N Hurst, Ellisa W Zhang, Hamilton D Green, Stefan Behr, Kirsten Jung, Maria Hadjifrangiskou
Two-component systems (TCSs) dictate many bacterial responses to environmental change via the activation of a membrane-embedded sensor kinase, which has molecular specificity for a cognate response regulator protein. However, although the majority of TCSs operate through seemingly strict cognate protein-protein interactions, there have been several reports of TCSs that violate this classical model of signal transduction. Our group has recently demonstrated that some of these cross-interacting TCSs function in a manner that imparts a fitness advantage to bacterial pathogens...
January 27, 2018: Journal of Membrane Biology
Aiswarya B Pawar, Durba Sengupta
The association of single transmembrane receptors, such as the ErbB receptors is a key event in initiating cell signaling networks. The interactions between these receptors have been well characterized for both ligand-driven and pre-formed dimers. However, the role of the membrane in modulating association is less well understood and assumes greater importance in light of altered membrane composition in diseased states. Here, we discuss how membrane composition has been observed to induce both structural and dynamic differences in receptor association...
January 19, 2018: Journal of Membrane Biology
Nikolay A Simakov, Maria G Kurnikova
The dependency of current-voltage characteristics of the α-hemolysin channel on the channel position within the membrane was studied using Poisson-Nernst-Planck theory of ion conductivity with soft repulsion between mobile ions and protein atoms (SP-PNP). The presence of the membrane environment also influences the protonation state of the residues at the boundary of the water-lipid interface. In this work, we predict that Asp and Lys residues at the protein rim change their protonation state upon penetration to the lipid environment...
January 16, 2018: Journal of Membrane Biology
Ran Friedman
Biomembranes assemble and operate at the interface with electrolyte solutions. Interactions between ions in solutions and the lipid affect the membrane structure, dynamics and electrostatic potential. In this article, I review some of the experimental and computational methods that are used to study membrane-ions interactions. Experimental methods that account for membrane-ion interactions directly and indirectly are presented first. Then, studies in which molecular dynamics simulations were used to gain an understanding of membrane-ion interactions are surveyed...
January 12, 2018: Journal of Membrane Biology
Denis G Knyazev, Roland Kuttner, Mirjam Zimmermann, Ekaterina Sobakinskaya, Peter Pohl
This review focusses on the energetics of protein translocation via the Sec translocation machinery. First we complement structural data about SecYEG's conformational rearrangements by insight obtained from functional assays. These include measurements of SecYEG permeability that allow assessment of channel gating by ligand binding and membrane voltage. Second we will discuss the power stroke and Brownian ratcheting models of substrate translocation and the role that the two models assign to the putative driving forces: (i) ATP (SecA) and GTP (ribosome) hydrolysis, (ii) interaction with accessory proteins, (iii) membrane partitioning and folding, (iv) proton motive force (PMF), and (v) entropic contributions...
January 12, 2018: Journal of Membrane Biology
Alina Asandei, Irina Schiopu, Corina Ciobanasu, Yoonkyung Park, Tudor Luchian
Herein, we report uni-molecular observations of electric potential- and electrolyte-dependent elasticity of poly(amidoamine) (PAMAM)-G1.5 dendrimers containing sodium carboxylate surface groups, using the electric field-assisted migration through the α-hemolysin nanopore (α-HL). Although at moderate transmembrane potentials the dendrimer (~ 2.5 nm in diameter) is sterically excluded from translocation across the constriction region of the nanopore (~ 1.5 nm in diameter), we found a threshold for its translocation that depends on both the electrolyte pH and ionic strength...
December 22, 2017: Journal of Membrane Biology
Filipe M Coreta-Gomes, Winchil L C Vaz, Maria J Moreno
The rate at which phospholipids equilibrate between different membranes and between the non-polar environments in biological fluids is of high importance in the understanding of biomembrane diversity, as well as in the development of liposomes for drug delivery. In this work, we characterize the rate of insertion into and desorption from POPC bilayers for a homologous series of amphiphiles with the fluorescent NBD group attached to phosphoethanolamines of different acyl chain lengths, NBD-diC n -PE with n = 6, 8, 10, and 12...
December 20, 2017: Journal of Membrane Biology
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