Challenges in the Accurate Modelling of Lipid Dynamics in Monolayers and Bilayers
Carmelo Tempra, Victor Cruces Chamorro, Titas Mandal, Salvatore Chiantia, Martin Vögele, Balazs Fabian, and Matti Javanainen
Publications
2024
A comparison of lipid diffusive dynamics in monolayers and bilayers in the context of interleaflet coupling
Titas Mandal, Nadine Brandt, Carmelo Tempra, Matti Javanainen, Balázs Fábián, and Salvatore Chiantia
Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?
Federica Scollo, Carmelo Tempra, Hüseyin Evci, Miguel Riopedre-Fernandez, Agnieszka Olżyńska, Matti Javanainen, Arunima Uday, Marek Cebecauer, Lukasz Cwiklik, Hector Martinez-Seara, Pavel Jungwirth, Piotr Jurkiewicz, and Martin Hof
2024 (pre-TAU)
Palmitoylation modifies transmembrane adaptor protein PAG for ordered lipid environment: A molecular dynamics simulation study
Maria Chiara Saija, Adéla Melcrová, Wojciech Pajerski, Itay Schachter, Matti Javanainen, Marek Cebecauer, and Lukasz Cwiklik
Exposure to aldehyde cherry e-liquid flavoring and its vaping byproduct disrupt pulmonary surfactant biophysical function
Alexia Martin, Carmelo Tempra, Yuefan Yu, Juho Liekkinen, Roma Thakker, Hayoung Lee, Berta de Santos Moreno, Ilpo Vattulainen, Christos Rossios, Matti Javanainen, and Jorge Bernardino de la Serna
Diffusion Analyses along Mean and Gaussian-Curved Membranes with CurD
Balázs Fábián and Matti Javanainen
Energetics of the Transmembrane Peptide Sorting by Hydrophobic Mismatch
Balázs Fábián, Matti Javanainen
Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field
Ricky Nencini, Carmelo Tempra, Denys Biriukov, Miguel Riopedre-Fernandez, Victor Cruces Chamorro, Jakub Polák, Philip E Mason, Daniel Ondo, Jan Heyda, OH Samuli Ollila, Pavel Jungwirth, Matti Javanainen, and Hector Martinez-Seara
Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?
Federica Scollo, Carmelo Tempra, Hüseyin Evci, Miguel Riopedre-Fernandez, Agnieszka Olżyńska, Matti Javanainen, Arunima Uday, Marek Cebecauer, Lukasz Cwiklik, Hector Martinez-Seara, Pavel Jungwirth, Piotr Jurkiewicz, and Martin Hof
2023 (pre-TAU)
Molecular view of ER membrane remodeling by the Sec61/TRAP translocon
Sudeep Karki, Matti Javanainen, Shahid Rehan, Dale Tranter, Juho Kellosalo, Juha T Huiskonen, Lotta Happonen, and Ville Paavilainen
Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints
Denys Biriukov, Matti Javanainen
Quantitative comparison against experiments reveals imperfections in force fields’ descriptions of popc–cholesterol interactions
Matti Javanainen, Peter Heftberger, Jesper J Madsen, Markus S Miettinen, Georg Pabst, and OH Samuli Ollila
Reduced binding of apoE4 to complement factor H promotes amyloid‐β oligomerization and neuroinflammation
Larisa Chernyaeva, Giorgio Ratti, Laura Teirilä, Satoshi Fudo, Uni Rankka, Anssi Pelkonen, Paula Korhonen, Katarzyna Leskinen, Salla Keskitalo, Kari Salokas, Christina Gkolfinopoulou, Katrina E Crompton, Matti Javanainen, Lotta Happonen, Markku Varjosalo, Tarja Malm, Ville Leinonen, Angeliki Chroni, Päivi Saavalainen, Seppo Meri, Tommi Kajander, Adam JM Wollman, Eija Nissilä, and Karita Haapasalo
Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion
Xinxin Woodward, Matti Javanainen, Balázs Fábián, and Christopher V Kelly
Protein crowding and cholesterol increase cell membrane viscosity in a temperature dependent manner
Balázs Fábián, Ilpo Vattulainen, and Matti Javanainen
Surfactant proteins SP-B and SP-C in pulmonary surfactant monolayers: Physical properties controlled by specific protein–lipid interactions
Juho Liekkinen, Agnieszka Olzynska, Lukasz Cwiklik, Jorge Bernardino de la Serna, Ilpo Vattulainen, and Matti Javanainen
2022 (pre-TAU)
Ionic strength and solution composition dictate the adsorption of cell-penetrating peptides onto phosphatidylcholine membranes
Man Thi Hong Nguyen, Denys Biriukov, Carmelo Tempra, Katarina Baxova, Hector Martinez-Seara, Huseyin Evci, Vandana Singh, Radek Sachl, Martin Hof, Pavel Jungwirth, Matti Javanainen, and Mario Vazdar
Accurate simulations of lipid monolayers require a water model with correct surface tension
Carmelo Tempra, OH Samuli Ollila, and Matti Javanainen
The two faces of the liquid ordered phase
Itay Schachter, Riku O Paananen, Balázs Fábián, Piotr Jurkiewicz, and Matti Javanainen
2021 (pre-TAU)
Inverse conformational selection in lipid–protein binding
Amélie Bacle, Pavel Buslaev, Rebeca Garcia-Fandino, Fernando Favela-Rosales, Tiago Mendes Ferreira, Patrick FJ Fuchs, Ivan Gushchin, Matti Javanainen, Anne M Kiirikki, Jesper J Madsen, Josef Melcr, Paula Milán Rodríguez, Markus S Miettinen, OH Samuli Ollila, Chris G Papadopoulos, Antonio Peón, Thomas J Piggot, Ángel Piñeiro, and Salla I Virtanen
Nonconverged constraints cause artificial temperature gradients in lipid bilayer simulations
Sebastian Thallmair, Matti Javanainen, Balázs Fábián, Hector Martinez-Seara, and Siewert J Marrink
Anisotropic diffusion of membrane proteins at experimental timescales
Matti Javanainen, Hector Martinez-Seara, Christopher V Kelly, Pavel Jungwirth, and Balázs Fábián
Martini 3: a general purpose force field for coarse-grained molecular dynamics
Paulo CT Souza, Riccardo Alessandri, Jonathan Barnoud, Sebastian Thallmair, Ignacio Faustino, Fabian Grünewald, Ilias Patmanidis, Haleh Abdizadeh, Bart MH Bruininks, Tsjerk A Wassenaar, Peter C Kroon, Josef Melcr, Vincent Nieto, Valentina Corradi, Hanif M Khan, Jan Domański, Matti Javanainen, Hector Martinez-Seara, Nathalie Reuter, Robert B Best, Ilpo Vattulainen, Luca Monticelli, Xavier Periole, D Peter Tieleman, Alex H de Vries, and Siewert J Marrink
2020 (pre-TAU)
Structural effects of cation binding to DPPC monolayers
Matti Javanainen, Wei Hua, Ondrej Tichacek, Pauline Delcroix, Lukasz Cwiklik, and Heather C Allen
Understanding the functional properties of lipid heterogeneity in pulmonary surfactant monolayers at the atomistic level
Juho Liekkinen, Berta de Santos Moreno, Riku O Paananen, Ilpo Vattulainen, Luca Monticelli, Jorge Bernardino de la Serna, and Matti Javanainen
Mcl-1 and Bok transmembrane domains: Unexpected players in the modulation of apoptosis
Estefanía Lucendo, Mónica Sancho, Fabio Lolicato, Matti Javanainen, Waldemar Kulig, Diego Leiva, Gerard Duart, Vicente Andreu-Fernández, Ismael Mingarro, and Mar Orzaez
A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization
Elise Duboue-Dijon, M Javanainen, P Delcroix, P Jungwirth, and H Martinez-Seara
Pulmonary surfactant lipid reorganization induced by the adsorption of the oligomeric surfactant protein B complex
Juho Liekkinen, Giray Enkavi, Matti Javanainen, Barbara Olmeda, Jesús Pérez-Gil, and Ilpo Vattulainen
Rotational diffusion of membrane proteins in crowded membranes
Matti Javanainen, OH Samuli Ollila, and Hector Martinez-Seara