Publications
2024 |
Bartoš, L.; Lund, M.; Vácha, R.: Enhanced Diffusion through Multivalency. submitted, link |
Linhartova, K.; Falginella, F.L.; Matl, M.; Šebesta, M.; Vácha, R.; Štefl, R.: Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7. Nature Communications 2024, 15, 9163, link |
Hazrati, M.K.; Vácha, R.: Membrane Adsorption Enhances Translocation of Antimicrobial Peptide Buforin 2. The Journal of Physical Chemistry B 2024, 128, 35, 8469–8476, link |
Deb, R.; Torres, M.D.T.; Boudný, M.; Koběrská, M.; Cappiello, F.; Popper, M.; Dvořáková Bendová, K.; Drabinová, M.; Hanáčková, A.; Jeannot, K.; Petřík, M.; Mangoni, M.L.; Balíková Novotná, G.; Mráz, M.; de la Fuente-Nunez, C.; Vácha, R.: Computational Design of Pore-Forming Peptides with Potent Antimicrobial and Anticancer Activities. Journal of Medicinal Chemistry 2024, 67, 16, 14040–14061, link |
Blasco S.; Sukeník, L.; Vácha, R.: Nanoparticle induced fusion of lipid membranes. Nanoscale 2024, 16, 10221-10229, link |
Bartoš, L.; Drabinová, M.; Vácha, R.: Optimizing properties of translocation-enhancing transmembrane proteins. Biophysical Journal 2024, 123, 1–13, link |
Biriukov, D.; Vácha, R.: Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050. ACS Physical Chemistry Au, 4(4), 302-313, link |
Morton, W.; Vácha, R.; Angioletti-Uberti, S.: Valency of Ligand–Receptor Binding from Pair Potentials. Journal of Chemical Theory and Computation 2024, 20, 7, 2901–2907, link |
Bartoš, L.; Vácha, R.: Peptide translocation across asymmetric phospholipid membranes. Biophysical Journal 2024, 123, 1-10, link |
Bartoš, L.; Menon, A.K.; Vácha, R.: Insertases Scramble Lipids: Molecular Simulations of MTCH2. Structure 2024, 32, 4, 505-510, link |
Pajtinka, P.; Vácha, R.: Amphipathic Helices Can Sense Both Positive and Negative Curvatures of Lipid Membranes. The Journal of Physical Chemistry Letters 2024, 15, 175−179, link |
2023 |
Jahn, H.; Bartoš, L.; Dearden, G.I.; Dittman, J.S.; Holthuis, J.C.M.; Vácha, R.; Menon, A.K.: Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase. Nature Communications 2023, 14, 8115, link |
2022 |
Semeraro, E.F.; Pajtinka, P.; Marx, L.; Kabelka, I.; Leber, R.; Lohner, K.; Vácha, R.; Pabst, G.: Magainin 2 and PGLa in Bacterial Membrane Mimics IV: Membrane Curvature and Partitioning. Biophysical Journal 2022, 121, 1-13, link |
Falginella, F.L.; Kravec, M.; Drabinová, M.; Paclíková, P., Bryja, V.; Vácha, R.: Binding of DEP domain to phospholipid membranes: More than just electrostatics. BBA - Biomembranes 2022, 1864 (10), 183983, link |
Khirsariya, P.; Pospíšil, P.; Maier, L.; Boudný, M.; Babáš, M.; Kroutil, O.; Mráz, M.; Vácha, R.; Paruch, K.: Synthesis and Profiling of Highly Selective Inhibitors of Methyltransferase DOT1L Based on Carbocyclic C-Nucleosides. Journal of Medicinal Chemistry 2022, 65 (7), 5701–5723, link |
Kabelka, I.; Georgiev, V.; Marx, L.; Pajtinka, P.; Lohner, K.; Pabst, G.; Dimova, R.; Vácha, R.: Magainin 2 and PGLa in Bacterial Membrane Mimics III: Membrane Fusion and Disruption. Biophysical Journal 2022, 121 (5), 852-861, link |
2021 |
Sukeník, L.; Mukhamedova, L.; Procházková, M.; Škubník, K.; Plevka, P.; Vácha, R.: Cargo Release from Nonenveloped Viruses and Virus-like Nanoparticles: Capsid Rupture or Pore Formation. ACS Nano 2021, 15 (12), 19233–19243, link |
Sarmento, M.J.; Owen, M.C.; Ricardo, J.C.; Chmelová, B.; Davidović, D.; Mikhalyov, I.; Gretskaya, N.; Hof, M.; Amaro, M.; Vácha, R.; Šachl, R.: The impact of the glycan headgroup on the nanoscopic segregation of gangliosides. Biophysical Journal 2021, 120 (24), 5530-5543 link |
Bartoš, L.; Kabelka, I.; Vácha, R.: Enhanced translocation of amphiphilic peptides across membranes by transmembrane proteins. Biophysical Journal 2021, 120 (11), 2296-2305, link |
Kabelka, I.; Vácha, R.: Advances in Molecular Understanding of α-helical Membrane-Active Peptides. Accounts of Chemical Research 2021, 54 (9), 2196–2204, link |
Procházková, M., Füzik, T., Grybchuk, D., Falginella, F., Podešvová, L., Yurchenko, V., Vácha, R., Plevka, P. Capsid structure of Leishmania RNA virus 1. Journal of Virology 2021, 95, e01957-20, link |
Jurásek, M.; Kumar, J.; Paclíková, P.; Kumari, A.; Tripsianes, K.; Bryja, V.; Vácha, R.: Phosphorylation-induced changes in the PDZ domain of Dishevelled 3. Scientific Reports 2021, 11, 1484, link |
Kabelka, I.; Brožek, R.; Vácha, R.: Selecting Collective Variables and Free Energy Methods for Peptide Translocation Across Membranes. Journal of Chemical Information and Modeling 2021, 61 (2), 819–830, link |
Škubník, K.; Sukeník, L.; Buchta, D.; Füzik, T.; Procházková, M.; Moravcová, J.; Šmerdová, L.; Přidal, A.; Vácha, R.; Plevka, P.: Capsid opening enables genome release of iflaviruses. Science Advances 2021, 7 (1), eabd7130, link |
2020 |
Brožek, R.; Kabelka, I.; Vácha, R.: Effect of Helical Kink on Peptide Translocation across Phospholipid Membranes. Journal of Physical Chemistry B 2020,124, 28, 5940-5947, link |
Brázda, R.; Krejčíková, M.; Kasiliauskaite, A.; Šmiřáková, E.; Klumpler, T.; Vácha, R.; Kubíček, K.; Štefl, R.: Yeast Spt6 reads multiple phosphorylation patterns of RNA Polymerase II C-terminal domain in vitro. Journal of Molecular Biology 2020, 432(14), 4092-4107, link |
Tuerkova, A.; Kabelka, I.; Králová, T.; Sukeník, L.; Pokorná, Š.; Hof, M.; Vácha, R.: Effect of helical kink in antimicrobial peptides on membrane pore formation. eLife 2020, 9, e47946, link |
Jurásek, M.; Flärdh, K.; Vácha, R.: Effect of membrane composition on DivIVA-membrane interaction. BBA Biomembranes 2020, 1862, 8, 183144, link |
Kabelka, I.; Pachler, M.; Prévost, S.; Letofsky-Papst, I.; Lohner, K.; Pabst, G.; Vácha, R.: Magainin 2 and PGLa in Bacterial Membrane Mimics II: Membrane Fusion and Sponge Phase Formation. Biophysical Journal 2020, 118, 3, 612-623, link |
2019 |
Pachler, M.; Kabelka, I.; Appavou, M.-S.; Lohner, K.; Vácha, R.; Pabst, G.: Magainin 2 and PGLa in Bacterial Membrane Mimics I: Peptide-Peptide and Lipid-Peptide Interactions. Biophysical Journal 2019, 117, 1858–1869, link |
Owen, M.C.; Karner, A.; Šachl, R.; Preiner, J.; Amaro, M.; Vácha, R.: Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments. Journal of Physical Chemistry B 2019, 123, 35, 7504-7517, link |
Buchta, D.; Füzik, T.; Hrebík, D.; Levdansky, Y.; Sukeník, L.; Mukhamedova, L.; Moravcová, J.; Vácha, R.; Plevka, P.: Enterovirus particles expel capsid pentamers to enable genome release. Nature Communications 2019, 10, 1138, link |
Harnoš, J.; Alonso Cañizal, M.C.A.; Jurásek, M.; Kumar, J.; Holler, C.; Schambony, A.; Hanáková, K.; Bernatík, O.; Zdráhal, Z.; Gömöryová, K.; Gybeľ, T.; Radaszkiewicz, T.W.; Kravec, M.; Trantírek, L.; Ryneš, J.; Dave, Z.; Fernández-Llamazares, A.I.; Vácha, R.; Tripsianes, K.; Hoffmann, C.; Bryja, V.: Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1. Nature Communications 2019, 10, 1804, link |
2018 |
Kabelka, I.; Vácha, R.: Optimal Hydrophobicity and Reorientation of Amphiphilic Peptides Translocating Through Membrane. Biophysical Journal 2018, 115 (6), 1045-1054, link |
Leber, R.; Pachler, M.; Kabelka, I.; Svoboda, I.; Koller, D.; Vácha, R.; Lohner, K.; Pabst, G.: Synergism of Antimicrobial Frog Peptides Couples to Membrane Intrinsic Curvature Strain. Biophysical Journal 2018, 114 (8), 1945-1954, link |
| Tesei, G.; Hellstrand, E.; Sanagavarapu, K.; Linse, S.; Sparr, E.; Vácha, R.; Lund, M.: Aggregate Size Dependence of Amyloid Adsorption onto Charged Interfaces. Langmuir 2018, 34 (4), 1266–1273, link |
2017 |
| Schubertová, V.; Martinez-Veracoechea, F.J.; Vácha, R.: Design of Multivalent Inhibitors for Preventing Cellular Uptake. Scientific Reports 2017, 7, 11689, link |
| Jurásek, M.; Vácha, R.: Self-assembled clusters of patchy rod-like molecules. Soft Matter 2017, 13, 7492 - 7497, link |
2016 |
| Amaro, M.; Sachl, R.; Aydogan, G.; Mikhalyov, I.I.; Vácha, R.; Hof, M.: GM1 Ganglioside Inhibits beta-Amyloid Oligomerization Induced by Sphingomyelin. Angewandte Chemie International Edition 2016, 55, 1-6, link |
2015 |
| Kabelka, I.; Vácha, R.: Optimal conditions for opening of membrane pore by amphiphilic peptides. The Journal of Chemical Physics 2015, 143, 243115, link |
| Schubertová, V.; Martinez-Veracoechea, F.J.; Vácha, R.: Influence of ligand distribution on uptake efficiency. Soft Matter 2015, 11, 2726-2730, link |
2014 |
| Vácha, R. ; Linse, S.; Lund, M.: Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides. Journal of American Chemical Society 2014, 136 (33), 11776-11782, link |
| Vácha, R. ; Frenkel, D.: Stability of Bicelles: A Simulation Study. Langmuir 2014, 30 (15), 4229-4235, link |
| Vácha, R. ; Frenkel, D.: Simulations Suggest Possible Novel Membrane Pore Structure. Langmuir 2014, 30 (5), 1304-1310, link |
| Vácha, R .; Uhlig, F.; Jungwirth, P.: Charges at aqueous interfaces: development of computational approaches in direct contact with experiment. Advances in Chemical Physics 2014, 155, 69-95, link |
2013 |
| Shi, Q.; Bergquist, K.-E.; Huo, R.; Li, J.; Lund, M.; Vácha, R.; Sundin, A.; Butkus, E.; Orentas, E.; Warnmark, K.: Composition- and Size-Controlled Cyclic Self-Assembly by Solvent and C60-Responsive Self-Sorting. Journal of American Chemical Society 2013, 135 (40), 15263-15268, link |
| Stenqvist, B.; Thuresson, A.; Kurut, A.; Vácha, R.; Lund, M.: Faunus - a flexible framework for Monte Carlo simulation. Molecular Simulation 2013, 39(14-15), 1233-1239, link |
2012 |
| Vácha, R .; Martinez-Veracoechea, F.J.; Frenkel, D.: Intracellular Release of Endocytosed Nanoparticles Upon a Change of Ligand-Receptor Interaction. ACS Nano 2012, 6 (12), 10598-10605, link |
| Bieler, N.S.; Knowles, T.P.J.; Frenkel, D.; Vácha, R.: Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations. PLoS Computational Biology 2012, 8 (10), e1002692, link |
| Vácha, R. ; Roke; S.: Sodium Dodecyl Sulfate at Water-Hydrophobic Interfaces: A Simulation Study. Journal of Physical Chemistry B 2012, 116 (39), 11936-11942, link |
| Vazdar, M.; Pluharová, E.; Mason, P.E.; Vácha, R.; Jungwirth, P.: Ions at Hydrophobic Aqueous Interfaces: Molecular Dynamics with Effective Polarization. Journal of Physical Chemistry Letters 2012, 3, 2087-2091, link |
| Berkowitz, M.L. and Vácha, R.: Aqueous Solutions at the Interface with Phospholipid Bilayers. Accounts of Chemical Research 2012, 45 (1), 74-82, link |
| Vácha, R .; Marsalek, O.; Willard, A.P.; Bonthuis, D.J.; Netz, R.R.; Jungwirth, P.: Charge Transfer between Water Molecules As the Possible Origin of the Observed Charging at the Surface of Pure Water. Journal of Physical Chemistry Letters 2012, 3 (1), 107-111, link |
| Pospíšil, M.; Kovár, P.; Vácha, R.; Svoboda, M.: Study of the betulin molecule in a water environment; ab initio and molecular simulation calculations. Journal of Molecular Modeling 2012, 18(1), 367-376 link |
2011 |
| Vácha, R. ; Martinez-Veracoechea, F.J.; Frenkel, D.: Receptor-Mediated Endocytosis of Nanoparticles of Various Shapes. Nano Letters 2011, 11 (12), 5391-5395, link |
| Vácha, R. ; Frenkel, D.: Relation between Molecular Shape and the Morphology of Self-Assembling Aggregates: A Simulation Study. Biophysical Journal 2011, 101, 1432-1439, link |
| Vácha, R. ; Rick, S.W.; Jungwirth, P.; de Beer, A.G.F.; de Aguiar, H.B.; Samson, J.-S.; Roke, S.: The Orientation and Charge of Water at the Hydrophobic Oil Droplet–Water Interface. Journal of American Chemical Society 2011, 133 (26), 10204-10210, link |
2010 |
| Wolff, W.; McKenna, J.; Vácha, R.; Zohrabi, M.; Gaire, B.; Carnesa, K.D.; Ben-Itzhak, I.: Three-dimensional energy profile measurement of a molecular ion beam by coincidence momentum imaging compared to a retarding field analyzer. Journal of Instrumentation 2010, P10006 link |
| Lund, M.; Jagoda-Cwiklik, B.; Woodward C.E.; Vácha, R.; Jungwirth, P.: Dielectric Interpretation of Specificity of Ion Pairing in Water. Journal of Physical Chemistry Letters 2010, 1 (1), 300-303, link |
| Vácha, R. ; Horinek, D.; Buchner, R.; Winter, B.; Jungwirth, P.: Comment on "An explanation for the charge on water's surface" by A. Gray-Weale and J. K. Beattie, Phys. Chem. Chem. Phys., 2009, 11, 10994 Physical Chemistry Chemical Physics 2010, 12 (42), 14362-14363, link |
| Vácha, R .; Jurkiewicz, P.; Petrov, M.; Berkowitz, M.L.; Böckmann, R. A.; Barucha-Kraszewska, J.; Hof, M.; Jungwirth, P.: Mechanism of Interaction of Monovalent Ions with Phosphatidylcholine Lipid Membranes. Journal of Physical Chemistry B 2010, 114 (29), 9504-9509, link |
2009 |
| Ottosson, N.; Vácha, R.; Aziz, E. F.; Pokapanich, W.; Eberhardt, W.; Svensson, S.; Öhrwall, G.; Jungwirth, P.; Björneholm, O.; Winter, B.: Large variations in the propensity of aqueous oxychlorine anions for the solution/vapor interface. Journal of Chemical Physics 2009, 131, 124706 link |
| Winter, B.; Faubel, M.; Vácha, R.; Jungwirth, P.: Reply to comments on Frontiers Article 'Behavior of hydroxide at the water/vapor interface'. Chemical Physics Letters 2009, 481, 19-21 link |
| Winter, B.; Faubel, M.; Vácha, R.; Jungwirth, P.: Behavior of hydroxide at the water/vapor interface. Chemical Physics Letters 2009, 474, 241-247 link |
| Heyda, J.; Pokorna, J.; Vrbka, L.; Vácha, R.; Jagoda-Cwiklik, B.; Konvalinka, J.; Jungwirth, P.; Vondrasek, J.: Ion specific effects of sodium and potassium on the catalytic activity of HIV-1 protease. Physical Chemistry Chemical Physics 2009, 11, 7599-7604 link |
| Vácha, R. ; Berkowitz, M. L.; Jungwirth, P.: Molecular Model of a Cell Plasma Membrane with an Asymmetric Multicomponent Composition: Water Permeation and Ion Effects. Biophysical Journal 2009, 96(11), 4493-4501 link |
| Vácha, R. ; Megyes, T.; Bako, I.; Pusztai, I.; Jungwirth, P.: Benchmarking polarizable molecular dynamics simulations of aqueous sodium hydroxide by diffraction measurements. Journal of Physical Chemistry A 2009, 113 (16), 4022-4027 link |
| Vácha, R. ; Siu, S. W. I.; Petrov, M.; Bockmann, R. A.; Barucha-Kraszewska, J.; Jurkiewicz, P.; Hof. M.; Berkowitz, M. L.; Jungwirth, P.: Effects of alkali cations and halide anions on the DOPC lipid membrane. Journal of Physical Chemistry B 2009, 113 (26), 7235-7243 link |
| Vlachy, N.; Jagoda-Cwiklik, B.; Vácha, R.; Touraud, D.; Jungwirth, P.; Kunz, W.: Hofmeister series and specific interactions of charged headgroups with aqueous ions. Advances in Colloid and Interface Science 2009, 146, 42-47 link |
2008 |
| Aziz, E. F.; Ottosson, N.; Eisebitt, S.; Jagoda-Cwiklik, B.; Vácha, R.; Jungwirth, P.; Winter, B.: Cation-specific interactions with carboxylate in amino acid and acetate aqueous s olutions: X-ray absorption and ab initio calculations. Journal of Physical Chemistry B 2008, 112, 12567-12570 link |
| Vácha, R. ; Buch, V.; Milet, A.; Devlin, J.P.; Jungwirth, P.: Response to Comment on Autoionization at the surface of neat water: is the top layer pH neutral, basic, or acidic? by J. K. Beattie, Phys. Chem. Chem. Phys., 2007, 9, DOI : 10.1039/b713702h Physical Chemistry Chemical Physics 2008, 10 (2), 332-333 link |
| Vácha, R. ; Horinek, D.; Berkowitz, M. L.; Jungwirth, P.: Hydronium and hydroxide at the interface between water and hydrophobic media. Physical Chemistry Chemical Physics 2008, 10, 4975-4980 link |
| Vácha, R. ; Zangi, R.; Engberts, J. B. F. N.; Jungwirth, P.: Water Structuring and Hydroxide Ion Binding at the Interface between Water and Hydrophobic Walls of Varying Rigidity a nd van der Waals Interactions. Journal of Physical Chemistry C 2008, 112 (20), 7689-7692 link |
| Vácha, R. ; Cwiklik, L.; Rezac, J.; Hobza, P.; Jungwirth, P.; Valsaraj, K.; Bahr, S.; Kempter, V.: Adsorption and Heterogeneous Reactions of Aromatic Hydrocarbons at Environmental Aqueous Surfaces. Journal of Physical Chemistry A 2008, 112 (22), 4942-4950 link |
| Siu, S. W. I; Vácha, R.; Jungwirth, P.; Bockmann, R. A.: Biomolecular simulations of membranes: Physical properties from different force fields. Journal of Chemical Physics 2008, 128, 125103, link |
| Lund, M.; Vácha, R.; Jungwirth, P.: Specific Ion-Binding to Macromolecules: Effects of Hydrophobicity and Ion Pairing. Langmuir 2008, 24(7), 3387-3391 link |
2007 |
| Jagoda-Cwiklik, B.; Vácha, R.; Lund, M.; Srebro, M.; Jungwirth, P.: Ion pairing as a possible clue for discriminating between sodium and potassium in biological and other complex environments. Journal of Physical Chemistry B 2007, 111, 14077-14079 link |
| Vácha, R. ; Buch, V.; Milet, A.; Devlin J.P.; Jungwirth, P.: Autoionization at the surface of neat water: is the top layer pH neutral, basic, or acidic? Physical Chemistry Chemical Physics 2007, 34, 4736-4747 link |
| Buch, V.; Milet, A.; Vácha, R.; Jungwirth, P.; Devlin J.P.: Water surface is acidic. Proceedings of the National Academy of Sciences of the United States of America 2007, 107 (18), 7342-7347 link |
2006 |
| Vrbka, L.; Vondrasek, J.; Jagoda-Cwiklik, B.; Vácha, R.; Jungwirth, P.: Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces. Proceedings of the National Academy of Sciences of the United States of America 2006, 103 (42), 15440-15444 link |
| Vácha, R. ; Jungwirth, P.; Chen, J.; Valsaraj, K.: Adsorption of polycyclic aromatic hydrocarbons at the air-water interface: Molecular dynamics simulations and experimental atmospheric observations. Physical Chemistry Chemical Physics 2006, 8 (38), 4461-4467 link |
| Minofar, B.; Vácha, R.; Wahab, A.; Mahiuddin, S.; Kunz, W.; Jungwirth, P.: Propensity for the air/water interface and ion pairing in magnesium acetate vs magnesium nitrate solutions: Molecular dynamics simulations and surface tension measurements. Journal of Physical Chemistry B 2006, 110 (32), 15939-15944 link |
2004 |
| Vácha, R. ; Slavicek, P.; Mucha, M.; Finlayson-Pitts, B. J.; Jungwirth, P.: Adsorption of atmospherically relevant gases at the air/water interface: Free energy profiles of aqueous solvation of N2, O2, O3, OH, H2O, HO2, and H2O2. Journal of Physical Chemistry A 2004, 108, 11573-11579 link |