Search Results - "Melcr, Josef"

Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes by Frallicciardi, Jacopo, Melcr, Josef, Siginou, Pareskevi, Marrink, Siewert J., Poolman, Bert

“…Cell membranes provide a selective semi-permeable barrier to the passive transport of molecules. This property differs greatly between organisms. While the…”
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Martini 3: a general purpose force field for coarse-grained molecular dynamics by Souza, Paulo C. T., Alessandri, Riccardo, Barnoud, Jonathan, Thallmair, Sebastian, Faustino, Ignacio, Grünewald, Fabian, Patmanidis, Ilias, Abdizadeh, Haleh, Bruininks, Bart M. H., Wassenaar, Tsjerk A., Kroon, Peter C., Melcr, Josef, Nieto, Vincent, Corradi, Valentina, Khan, Hanif M., Domański, Jan, Javanainen, Matti, Martinez-Seara, Hector, Reuter, Nathalie, Best, Robert B., Vattulainen, Ilpo, Monticelli, Luca, Periole, Xavier, Tieleman, D. Peter, de Vries, Alex H., Marrink, Siewert J.

“…The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 ( http://cgmartini.nl ), with…”
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Accurate Biomolecular Simulations Account for Electronic Polarization by Melcr, Josef, Piquemal, Jean-Philip

“…In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations…”
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Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers by Antila, Hanne, Buslaev, Pavel, Favela-Rosales, Fernando, Ferreira, Tiago M, Gushchin, Ivan, Javanainen, Matti, Kav, Batuhan, Madsen, Jesper J, Melcr, Josef, Miettinen, Markus S, Määttä, Jukka, Nencini, Ricky, Ollila, O. H. Samuli, Piggot, Thomas J

“…Phosphatidylserine (PS) is a negatively charged lipid type commonly found in eukaryotic membranes, where it interacts with proteins via nonspecific…”
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Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance by Melcr, Josef, Bonhenry, Daniel, Timr, Štěpán, Jungwirth, Pavel

“…Two approaches for modeling of the transmembrane potential, as present in all eukaryotic cells, are examined in detail and compared with each other. One…”
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Lateral membrane organization as target of an antimicrobial peptidomimetic compound by Melcrová, Adéla, Maity, Sourav, Melcr, Josef, de Kok, Niels A. W., Gabler, Mariella, van der Eyden, Jonne, Stensen, Wenche, Svendsen, John S. M., Driessen, Arnold J. M., Marrink, Siewert J., Roos, Wouter H.

“…Antimicrobial resistance is one of the leading concerns in medical care. Here we study the mechanism of action of an antimicrobial cationic tripeptide,…”
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Membrane manipulation by free fatty acids improves microbial plant polyphenol synthesis by Tharmasothirajan, Apilaasha, Melcr, Josef, Linney, John, Gensch, Thomas, Krumbach, Karin, Ernst, Karla Marlen, Brasnett, Christopher, Poggi, Paola, Pitt, Andrew R., Goddard, Alan D., Chatgilialoglu, Alexandros, Marrink, Siewert J., Marienhagen, Jan

“…Microbial synthesis of nutraceutically and pharmaceutically interesting plant polyphenols represents a more environmentally friendly alternative to chemical…”
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Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools by Bondar, Alexey, Rybakova, Olga, Melcr, Josef, Dohnálek, Jan, Khoroshyy, Petro, Ticháček, Ondřej, Timr, Štěpán, Miclea, Paul, Sakhi, Alina, Marková, Vendula, Lazar, Josef

“…Fluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well as obtaining quantitative information…”
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Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization by Melcr, Josef, Martinez-Seara, Hector, Nencini, Ricky, Kolafa, Jiří, Jungwirth, Pavel, Ollila, O. H. Samuli

“…Binding affinities and stoichiometries of Na+ and Ca2+ ions to phospholipid bilayers are of paramount significance in the properties and functionality of…”
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Improved Cation Binding to Lipid Bilayers with Negatively Charged POPS by Effective Inclusion of Electronic Polarization by Melcr, Josef, Ferreira, Tiago M, Jungwirth, Pavel, Ollila, O. H. Samuli

“…Phosphatidylserine (PS) lipids are important signaling molecules and the most common negatively charged lipids in eukaryotic membranes. The signaling can be…”
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Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations by Nemchinova, Mariia, Melcr, Josef, Wassenaar, Tsjerk A, Marrink, Siewert J, Guskov, Albert

“…The CorA family of proteins plays a housekeeping role in the homeostasis of divalent metal ions in many bacteria and archaea as well as in mitochondria of…”
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Dual Resolution Membrane Simulations Using Virtual Sites by Liu, Yang, De Vries, Alex H, Barnoud, Jonathan, Pezeshkian, Weria, Melcr, Josef, Marrink, Siewert J

“…All-atomistic (AA) and coarse-grain (CG) simulations have been successfully applied to investigate a broad range of biomolecular processes. However, the…”
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Inverse Conformational Selection in Lipid–Protein Binding by Bacle, Amélie, Buslaev, Pavel, Garcia-Fandino, Rebeca, Favela-Rosales, Fernando, Mendes Ferreira, Tiago, Fuchs, Patrick F. J, Gushchin, Ivan, Javanainen, Matti, Kiirikki, Anne M, Madsen, Jesper J, Melcr, Josef, Milán Rodríguez, Paula, Miettinen, Markus S, Ollila, O. H. Samuli, Papadopoulos, Chris G, Peón, Antonio, Piggot, Thomas J, Piñeiro, Ángel, Virtanen, Salla I

“…Interest in lipid interactions with proteins and other biomolecules is emerging not only in fundamental biochemistry but also in the field of nanobiotechnology…”
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Estimation of Transition-Metal Empirical Parameters for Molecular Mechanical Force Fields by Šebesta, Filip, Sláma, Vladislav, Melcr, Josef, Futera, Zdeněk, Burda, Jaroslav V

“…Force-field parameters of the first row transition metals together with a few additional common elements such as those from the second (Rh, Ru) and third (Hg,…”
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Distinct Interactions of Sodium and Calcium Cations and Neutral Phospholipid Membranes and How to Simulate Them by Martinez-Seara, Hector, Javanainen, Matti, Melcrová, Adéla, Jurkiewicz, Piotr, Jungwirth, Pavel, Magarkar, Aniket, Hof, Martin, Melcr, Josef, Nencini, Ricky, Ollila, Samuli O.

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Adaptive response to wine selective pressures shapes the genome of a Saccharomyces interspecies hybrid by Lairón-Peris, María, Castiglioni, Gabriel L, Routledge, Sarah J, Alonso-Del-Real, Javier, Linney, John A, Pitt, Andrew R, Melcr, Josef, Goddard, Alan D, Barrio, Eladio, Querol, Amparo

“…During industrial processes, yeasts are exposed to harsh conditions, which eventually lead to adaptation of the strains. In the laboratory, it is possible to…”
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Accurate biomolecular simulations account for electronic polarization by Melcr, Josef, Piquemal, Jean-Philip

“…Front. Mol. Biosci., 2019, 6, 143 In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of…”
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