Robert Vácha, Ph.D.

Publications that are part of the Web of Science database, possibly also other publications chosen by authors.

2021

• Bartos, L; Kabelka, I; Vacha, R, 2021: Enhanced translocation of amphiphilic peptides across membranes by transmembrane proteins. BIOPHYSICAL JOURNAL 120(11), p. 2296 - 2305, doi: 10.1016/j.bpj.2021.04.005
• Prochazkova, M; Fuzik, T; Grybchuk, D; Falginella, FL; Podesvova, L; Yurchenko, V; Vacha, R; Plevka, P, 2021: Capsid Structure of Leishmania RNA Virus 1. JOURNAL OF VIROLOGY 95(3), doi: 10.1128/JVI.01957-20
• Jurasek, M; Kumar, J; Paclikova, P; Kumari, A; Tripsianes, K; Bryja, V; Vacha, R, 2021: Phosphorylation-induced changes in the PDZ domain of Dishevelled 3. SCIENTIFIC REPORTS 11(1), doi: 10.1038/s41598-020-79398-5
• Kabelka, I; Brozek, R; Vacha, R, 2021: Selecting Collective Variables and Free-Energy Methods for Peptide Translocation across Membranes. JOURNAL OF CHEMICAL INFORMATION AND MODELING 61(2), p. 819 - 830, doi: 10.1021/acs.jcim.0c01312
• Skubnik, K; Sukenik, L; Buchta, D; Fuzik, T; Prochazkova, M; Moravcova, J; Smerdova, L; Pridal, A; Vacha, R; Plevka, P, 2021: Capsid opening enables genome release of iflaviruses. SCIENCE ADVANCES 7(1), doi: 10.1126/sciadv.abd7130
• Kabelka, I; Vacha, R, 2021: Advances in Molecular Understanding of alpha-Helical Membrane-Active Peptides. ACCOUNTS OF CHEMICAL RESEARCH 54(9), p. 2196 - 2204, doi: 10.1021/acs.accounts.1c00047
• Labajova, N; Baranova, N; Jurasek, M; Vacha, R; Loose, M; Barak, I, 2021: Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein DivIVA. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 22(15), doi: 10.3390/ijms22158350

2020

• Kabelka, I; Pachler, M; Prevost, S; Letofsky-Papst, I; Lohner, K; Pabst, G; Vacha, R, 2020: Synergism between Magainin 2 and PGLa in Bacterial Membrane Mimics Leads to Membrane Fusion and Sponge Phase Formation. BIOPHYSICAL JOURNAL 118(3), p. 343A - 343A
• Tuerkova, A; Kabelka, I; Kralova, T; Sukenik, L; Pokorna, S; Hof, M; Vacha, R, 2020: Effect of helical kink in antimicrobial peptides on membrane pore formation. ELIFE 9, doi: 10.7554/eLife.47946
• Jurasek, M; Flardh, K; Vacha, R, 2020: Effect of membrane composition on DivIVA-membrane interaction. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 1862(8), doi: 10.1016/j.bbamem.2019.183144
• Brozek, R; Kabelka, I; Vacha, R, 2020: Effect of Helical Kink on Peptide Translocation across Phospholipid Membranes. JOURNAL OF PHYSICAL CHEMISTRY B 124(28), p. 5940 - 5947, doi: 10.1021/acs.jpcb.0c03291
• Brazda, P; Krejcikova, M; Kasiliauskaite, A; Smirakova, E; Klumpler, T; Vacha, R; Kubicek, K; Stefl, R, 2020: Yeast Spt6 Reads Multiple Phosphorylation Patterns of RNA Polymerase II C-Terminal Domain In Vitro. JOURNAL OF MOLECULAR BIOLOGY 432(14), p. 4092 - 4107, doi: 10.1016/j.jmb.2020.05.007
• Kabelka, I; Pachler, M; Prevost, S; Letofsky-Papst, I; Lohner, K; Pabst, G; Vacha, R, 2020: Magainin 2 and PGLa in Bacterial Membrane Mimics II: Membrane Fusion and Sponge Phase Formation. BIOPHYSICAL JOURNAL 118(3), p. 612 - 623, doi: 10.1016/j.bpj.2019.12.019

2019

• Pachler, M; Kabelka, I; Appavou, MS; Lohner, K; Vacha, R; Pabst, G, 2019: Magainin 2 and PGLa in Bacterial Membrane Mimics I: Peptide-Peptide and Lipid-Peptide Interactions. BIOPHYSICAL JOURNAL 117(10), p. 1858 - 1869, doi: 10.1016/j.bpj.2019.10.022
• Buchta, D; Füzik, T; Hrebík, D; Levdansky, Y; Sukeník, L; Mukhamedova, L; Moravcová, J; Vácha, R; Plevka, P., 2019: Enterovirus particles expel capsid pentamers to enable genome release. NATURE COMMUNICATIONS , doi: 10.1038/s41467-019-09132-x
• Harnos, J; Canizal, MCA; Jurasek, M; Kumar, J; Holler, C; Schambony, A; Hanakova, K; Bernatik, O; Zdrahal, Z; Gomoryova, K; Gybel, T; Radaszkiewicz, TW; Kravec, M; Trantirek, L; Rynes, J; Dave, Z; Fernandez-Llamazares, AI; Vacha, R; Tripsianes, K; Hoffmann, C; Bryja, V, 2019: Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1. NATURE COMMUNICATIONS 10, doi: 10.1038/s41467-019-09651-7
• Turkova, A; Kabelka, I; Kralova, T; Sukenik, L; Pokorna, S; Hof, M; Vacha, R, 2019: Kink in Helical Peptides Affects Membrane Pore Formation. BIOPHYSICAL JOURNAL 116(3), p. 512A - 512A, doi: 10.1016/j.bpj.2018.11.2760
• Pachler, M; Kabelka, I; Leber, R; Letofsky-Papst, I; Lohner, K; Vacha, R; Pabst, G, 2019: Synergism of Magainins is Not Coupled to the Formation of a Well-Defined Peptide Pore. BIOPHYSICAL JOURNAL 116(3), p. 44A - 44A, doi: 10.1016/j.bpj.2018.11.280
• Owen, MC; Karner, A; Sachl, R; Preiner, J; Amaro, M; Vacha, R, 2019: Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments. JOURNAL OF PHYSICAL CHEMISTRY B 123(35), p. 7504 - 7517, doi: 10.1021/acs.jpcb.9b05095

2018

• Tesei, G; Hellstrand, E; Sanagavarapu, K; Linse, S; Sparr, E; Vacha, R; Lund, M, 2018: Aggregate Size Dependence of Amyloid Adsorption onto Charged Interfaces. LANGMUIR 34(4), p. 1266 - 1273, doi: 10.1021/acs.langmuir.7b03155
• Leber, R; Pachler, M; Kabelka, I; Svoboda, I; Enkoller, D; Vacha, R; Lohner, K; Pabst, G, 2018: Synergism of Antimicrobial Frog Peptides Couples to Membrane Intrinsic Curvature Strain. BIOPHYSICAL JOURNAL 114(8), p. 1945 - 1954, doi: 10.1016/j.bpj.2018.03.006
• Kabelka, I; Vacha, R, 2018: Optimal Hydrophobicity and Reorientation of Amphiphilic Peptides Translocating through Membrane. BIOPHYSICAL JOURNAL 115(6), p. 1045 - 1054, doi: 10.1016/j.bpj.2018.08.012
• Vacha, R; Kabelka, I; Brozek, R, 2018: Translocation of amphiphilic peptides across phospholipid membranes. FEBS OPEN BIO 8, p. 25 - 25
• Kabelka, I; Brozek, R; Vacha, R, 2018: Multivalent Inhibitors Preventing Uptake of Virus-Like Particles. BIOPHYSICAL JOURNAL 114(3), p. 279A - 279A, doi: 10.1016/j.bpj.2017.11.1607

2017

• Kabelka, I; Vacha, R, 2017: Peptide features determining its ability of translocation and membrane pore formation. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 46, p. S386 - S386
• Amaro, M; Sachl, R; Vacha, R; Hof, M, 2017: Unifying view on the impact of GM1 in the oligomerisation of membrane bound A beta monomers. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 46, p. S236 - S236
• Schubertova, V; Martinez-Veracoechea, FJ; Vacha, R, 2017: Design of Multivalent Inhibitors for Preventing Cellular Uptake. SCIENTIFIC REPORTS 7, doi: 10.1038/s41598-017-11735-7
• Jurasek, M; Vacha, R, 2017: Self-assembled clusters of patchy rod-like molecules. SOFT MATTER 13(41), p. 7492 - 7497, doi: 10.1039/c7sm01384a

2016

• Amaro, M; Sachl, R; Aydogan, G; Mikhalyov, I; Vacha, R; Hof, M, 2016: The role of ganglioside GM1 and sphingomyelin in the oligomerisation of beta-amyloid at physiological conditions: a single molecule study. FEBS JOURNAL 283, p. 71 - 71
• Amaro, M; Sachl, R; Aydogan, G; Mikhalyov, II; Vacha, R; Hof, M, 2016: GM(1) Ganglioside Inhibits beta-Amyloid Oligomerization Induced by Sphingomyelin. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 55(32), p. 9411 - 9415, doi: 10.1002/anie.201603178

2015

• Schubertova, V; Martinez-Veracoechea, FJ; Vacha, R, 2015: Influence of ligand distribution on uptake efficiency. SOFT MATTER 11(14), p. 2726 - 2730, doi: 10.1039/c4sm02815e
• KABELKA, I; VACHA, R, 2015: Optimal conditions for opening of membrane pore by amphiphilic peptides. THE JOURNAL OF CHEMICAL PHYSICS 143(24), p. 243115 -

2014

• Vacha, R; Linse, S; Lund, M, 2014: Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 136(33), p. 11776 - 11782, doi: 10.1021/ja505502e
• Vacha, R; Frenkel, D, 2014: Stability of Bicelles: A Simulation Study. LANGMUIR 30(15), p. 4229 - 4235, doi: 10.1021/la4048159
• Vacha, R; Frenkel, D, 2014: Simulations Suggest Possible Novel Membrane Pore Structure. LANGMUIR 30(5), p. 1304 - 1310, doi: 10.1021/la402727a
• Vacha, R; Uhlig, F; Jungwirth, P, 2014: CHARGES AT AQUEOUS INTERFACES: DEVELOPMENT OF COMPUTATIONAL APPROACHES IN DIRECT CONTACT WITH EXPERIMENT. ADVANCES IN CHEMICAL PHYSICS, VOL 155 155, p. 69 - 95

2013

• Stenqvist, B; Thuresson, A; Kurut, A; Vacha, R; Lund, M, 2013: Faunus - a flexible framework for Monte Carlo simulation. MOLECULAR SIMULATION 39(14-15), p. 1205 - 1211, doi: 10.1080/08927022.2013.828207
• Shi, QX; Bergquist, KE; Huo, RP; Li, JL; Lund, M; Vacha, R; Sundin, A; Butkus, E; Orentas, E; Warnmark, K, 2013: Composition- and Size-Controlled Cyclic Self-Assembly by Solvent- and C-60-Responsive Self-Sorting. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 135(40), p. 15263 - 15268, doi: 10.1021/ja408582w
• Berkowitz, M; Irudayam, S; Santo, K; Vacha, R, 2013: Structural and thermodynamic characteristics of melittin-phospholipid bilayer interaction: Results from computer simulations. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 245
• Vacha, R; Martinez-Veracoechea, FJ; Frenkel, D, 2013: Challenges in Nanoparticle Delivery: Cellular Uptake and Intracellular Escape. BIOPHYSICAL JOURNAL 104(2), p. 622A - 622A

2012

• Vazdar, M; Pluharova, E; Mason, PE; Vacha, R; Jungwirth, P, 2012: Ions at Hydrophobic Aqueous Interfaces: Molecular Dynamics with Effective Polarization. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 3(15), p. 2087 - 2091, doi: 10.1021/jz300805b
• Pospisil, M; Kovar, P; Vacha, R; Svoboda, M, 2012: Study of the betulin molecule in a water environment; ab initio and molecular simulation calculations. JOURNAL OF MOLECULAR MODELING 18(1), p. 367 - 376, doi: 10.1007/s00894-011-1055-y
• Berkowitz, ML; Vacha, R, 2012: Aqueous Solutions at the Interface with Phospholipid Bilayers. ACCOUNTS OF CHEMICAL RESEARCH 45(1), p. 74 - 82, doi: 10.1021/ar200079x
• Bieler, NS; Knowles, TPJ; Frenkel, D; Vacha, R, 2012: Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations. PLOS COMPUTATIONAL BIOLOGY 8(10), p. ´nestrankovano´ - , doi: 10.1371/journal.pcbi.1002692
• Vacha, R; Marsalek, O; Willard, AP; Bonthuis, DJ; Netz, RR; Jungwirth, P, 2012: Charge Transfer between Water Molecules As the Possible Origin of the Observed Charging at the Surface of Pure Water. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 3(1), p. 107 - 111, doi: 10.1021/jz2014852
• Vacha, R; Martinez-Veracoechea, FJ; Frenkel, D, 2012: Intracellular Release of Endocytosed Nanoparticles Upon a Change of Ligand-Receptor Interaction. ACS NANO 6(12), p. 10598 - 10605, doi: 10.1021/nn303508c
• Vacha, R; Roke, S, 2012: Sodium Dodecyl Sulfate at Water-Hydrophobic Interfaces: A Simulation Study. JOURNAL OF PHYSICAL CHEMISTRY B 116(39), p. 11936 - 11942, doi: 10.1021/jp304900z
• Vacha, R; Marsalek, O; Willard, AP; Bonthuis, DJ; Netz, RR; Jungwirth, P, 2012: Charge transfer between water molecules leads to weak charging at the surface of pure water. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 244

2011

• Vacha, R; Jungwirth, P; Roke, S; Frenkel, D, 2011: Sodium dodecyl sulfate at water/hydrophobic interfaces. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 242
• Vacha, R; Rick, SW; Jungwirth, P; de Beer, AGF; de Aguiar, HB; Samson, JS; Roke, S, 2011: The Orientation and Charge of Water at the Hydrophobic Oil Droplet-Water Interface. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 133(26), p. 10204 - 10210, doi: 10.1021/ja202081x
• Vacha, R; Frenkel, D, 2011: Relation between Molecular Shape and the Morphology of Self-Assembling Aggregates: A Simulation Study. BIOPHYSICAL JOURNAL 101(6), p. 1432 - 1439, doi: 10.1016/j.bpj.2011.07.046
• Vacha, R; Martinez-Veracoechea, FJ; Frenkel, D, 2011: Receptor-Mediated Endocytosis of Nanoparticles of Various Shapes. NANO LETTERS 11(12), p. 5391 - 5395, doi: 10.1021/nl2030213

2010

• Wolff, W; McKenna, J; Vacha, R; Zohrabi, M; Gaire, B; Carnes, KD; Ben-Itzhak, I, 2010: Three-dimensional energy profile measurement of a molecular ion beam by coincidence momentum imaging compared to a retarding field analyzer. JOURNAL OF INSTRUMENTATION 5, doi: 10.1088/1748-0221/5/10/P10006
• Lund, M; Jagoda-Cwiklik, B; Woodward, CE; Vacha, R; Jungwirth, P, 2010: Dielectric Interpretation of Specificity of Ion Pairing in Water. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 1(1), p. 300 - 303, doi: 10.1021/jz900151f
• Vacha, R; Jurkiewicz, P; Petrov, M; Berkowitz, ML; Bockmann, RA; Barucha-Kraszewska, J; Hof, M; Jungwirth, P, 2010: Mechanism of Interaction of Monovalent Ions with Phosphatidylcholine Lipid Membranes. JOURNAL OF PHYSICAL CHEMISTRY B 114(29), p. 9504 - 9509, doi: 10.1021/jp102389k
• Vacha, Robert; Horinek, Dominik; Buchner, Richard; Winter, Bernd; Jungwirth, Pavel, 2010: 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 12(42), p. 14362 - 14363

2009

• Winter, Bernd; Faubel, Manfred; Vacha, Robert; Jungwirth, Pavel, 2009: Reply to comments on Frontiers Article ´Behavior of hydroxide at the water/vapor interface´. CHEMICAL PHYSICS LETTERS 481(2014-03-01T00:00:00.000), p. 19 - 21
• Vacha, Robert; Berkowitz, Max L.; Jungwirth, Pavel, 2009: Molecular Model of a Cell Plasma Membrane With an Asymmetric Multicomponent Composition: Water Permeation and Ion Effects. BIOPHYSICAL JOURNAL 96(11), p. 4493 - 4501
• Ottosson, Niklas; Vacha, Robert; Aziz, Emad F.; Pokapanich, Wandared; Eberhardt, Wolfgang; Svensson, Svante; Ohrwall, Gunnar; Jungwirth, Pavel; Bjorneholm, Olle; Winter, Bernd, 2009: Large variations in the propensity of aqueous oxychlorine anions for the solution/vapor interface. JOURNAL OF CHEMICAL PHYSICS 131(12)
• Vacha, Robert; Siu, Shirley W. I.; Petrov, Michal; Boeckmann, Rainer A.; Barucha-Kraszewska, Justyna; Jurkiewicz, Piotr; Hof, Martin; Berkowitz, Max L.; Jungwirth, Pavel, 2009: Effects of Alkali Cations and Halide Anions on the DOPC Lipid Membrane. JOURNAL OF PHYSICAL CHEMISTRY A 113(26), p. 7235 - 7243
• Vlachy, Nina; Jagoda-Cwiklik, Barbara; Vacha, Robert; Touraud, Didier; Jungwirth, Pavel; Kunz, Werner, 2009: Hofmeister series and specific interactions of charged headgroups with aqueous ions. ADVANCES IN COLLOID AND INTERFACE SCIENCE 146(2014-02-01T00:00:00.000), p. 42 - 47
• Heyda, Jan; Pokorna, Jana; Vrbka, Lubos; Vacha, Robert; Jagoda-Cwiklik, Barbara; Konvalinka, Jan; Jungwirth, Pavel; Vondrasek, Jiri, 2009: Ion specific effects of sodium and potassium on the catalytic activity of HIV-1 protease. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 11(35), p. 7599 - 7604
• Heyda, Jan; Vacha, Robert; Vondrasek, Jiri; Jungwirth, Pavel, 2009: Ions at aqueous interfaces: From water surface to hydrated proteins. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 237
• Winter, Bernd; Faubel, Manfred; Vacha, Robert; Jungwirth, Pavel, 2009: Behavior of hydroxide at the water/vapor interface. CHEMICAL PHYSICS LETTERS 474(2014-06-04T00:00:00.000), p. 241 - 247
• Vacha, Robert; Megyes, Tunde; Bako, Imre; Pusztai, Laszlo; Jungwirth, Pavel, 2009: Benchmarking Polarizable Molecular Dynamics Simulations of Aqueous Sodium Hydroxide by Diffraction Measurements. JOURNAL OF PHYSICAL CHEMISTRY A 113(16), p. 4022 - 4027

• Peptide Killers of Bacteria, , 2022 - 2026
• Peptide Killers of Bacteria, , 2020 - 2025
• Protein Affinity and Selectivity to Cellular Membranes, Grantová agentura ČR, 2020 - 2022
• Amphiphilic Peptides at Phospholipid Membranes (GA17-11571S), Grantová agentura ČR, 2017 - 2019
• Computational chemistry for Wnt signaling pathway (MUNI/G/1100/2016), Masarykova univerzita, 2017 - 2019
• Toxicita a aktivita antimikrobiálních peptidů, Masarykova univerzita, 2018 - 2019