Matti Javanainen

Publications

• Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers
• Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations
• Accurate Simulations of Lipid Monolayers Require a Water Model With Correct Surface Tension
• The Two Faces of the Liquid Ordered Phase
• The Two Faces of the Liquid Ordered Phase
• Pulmonary Surfactant Lipid Reorganization Induced by the Adsorption of the Oligomeric Surfactant Protein B Complex
• Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion
• Comment on "Capturing phase behavior of ternary lipid mixtures with a refined Martini coarse-grained force field"
• Martini 3: a general purpose force field for coarse-grained molecular dynamics
• Structural Effects of Cation Binding to DPPC Monolayers
• Protein Crowding and Cholesterol Increase Cell Membrane Viscosity in a Temperature Dependent Manner
• Accurate Simulations of Lipid Monolayers Require a Water Model with Correct Surface Tension
• Ionic Strength and Solution Composition Dictate the Adsorption of Cell-Penetrating Peptides onto Phosphatidylcholine Membranes
• Surfactant Proteins SP-B and SP-C in Pulmonary Surfactant Monolayers: Physical Properties Controlled by Specific Protein–Lipid Interactions
• Molecular view of ER membrane remodeling by the Sec61/TRAP translocon
• Protein Crowding and Cholesterol Increase Cell Membrane Viscosity in a Temperature Dependent Manner
• Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level
• Efficient Simulations of Membrane and Solvent Asymmetry With Flat-Bottom Restraints
• Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion
• Molecular view of ER membrane remodeling by the Sec61/TRAP translocon
• Correction to “On Atomistic Models for Molecular Oxygen”
• Surfactant Proteins SP-B and SP-C in Pulmonary Surfactant Monolayers: Physical Properties Controlled by Specific Protein–Lipid Interactions
• Signal peptide mimicry primes Sec61 for client-selective inhibition
• Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints
• Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions
• Reduced binding of apoE4 to complement factor H promotes amyloid-beta oligomerization and neuroinflammation
• The Sec61/TRAP Translocon Scrambles Lipids
• Excessive aggregation of membrane proteins in the Martini model
• Diffusion of Integral Membrane Proteins in Protein-Rich Membranes
• Quantitative Assessment of Methods Used To Obtain Rate Constants from Molecular Dynamics Simulations—Translocation of Cholesterol across Lipid Bilayers
• How to minimize dye-induced perturbations while studying biomembrane structure and dynamics
• Arginine-rich cell-penetrating peptides induce membrane multilamellarity and subsequently enter via formation of a fusion pore
• The Devil Is in the Details: What Do We Really Track in Single-Particle Tracking Experiments of Diffusion in Biological Membranes?
• Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance
• Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions
• Rapid diffusion of cholesterol along polyunsaturated membranes via deep dives
• Crystalline Wax Esters Regulate the Evaporation Resistance of Tear Film Lipid Layers Associated with Dry Eye Syndrome
• Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers
• Rotational Diffusion of Membrane Proteins in Crowded Membranes
• Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level
• A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization
• Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?
• Mcl-1 and Bok transmembrane domains: Unexpected players in the modulation of apoptosis
• Structural Effects of Cation Binding to DPPC Monolayers
• Anisotropic diffusion of membrane proteins at experimental timescales
• Palmitoylation modifies transmembrane adaptor protein PAG for ordered lipid environment
• Inverse Conformational Selection in Lipid–Protein Binding
• Accurate Simulations of Lipid Monolayers Require a Water Model With Correct Surface Tension
• The Two Faces of the Liquid Ordered Phase
• Exposure to Aldehyde Cherry e-Liquid Flavoring and Its Vaping Byproduct Disrupt Pulmonary Surfactant Biophysical Function
• Nanoscale Membrane Domain Formation Driven by Cholesterol
• Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol
• Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle
• Protein crowding in lipid bilayers gives rise to non-Gaussian anomalous lateral diffusion of phospholipids and proteins
• Membrane omega-3 fatty acids modulate the oligomerisation kinetics of adenosine A2A and dopamine D2 receptors
• Two cations, two mechanisms: interactions of sodium and calcium with zwitterionic lipid membranes
• The Effect of Membrane Polyunsaturated Fatty Acids on Receptor Partitioning to Ordered Domains
• Cell Membrane Composition Affects GPCR Aggregation
• What Happens for Sterol Dynamics When Cholesterol is Enzymatically Oxidized?
• Flip-Flops of Lipids in the Absence of Atp: Role of Membrane Proteins
• Characterisation of Coexisting Liquid Phases in Mixtures of Dipalmitoylphosphatidylcholine and Cholesterol
• Anomalous and normal diffusion of proteins and lipids in crowded lipid membranes
• Do Lipids Retard the Evaporation of the Tear Fluid?
• Anomalous Diffusion of Phospholipids and Cholesterols in a Lipid Bilayer and its Origins
• Universal Method for Embedding Proteins into Complex Lipid Bilayers for Molecular Dynamics Simulations
• How well does cholesteryl hemisuccinate mimic cholesterol in saturated phospholipid bilayers?
• How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations
• Open Collaboration that uses NMR Data to Judge the Correctness of Phospholipid Glycerol and Head Group Structures in Molecular Dynamics Simulations
• Free Volume Theory Applied to Lateral Diffusion in Langmuir Monolayers: Atomistic Simulations for a Protein-Free Model of Lung Surfactant
• How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: β 2 -Adrenergic Receptor in the Spotlight
• Mechanism for translocation of fluoroquinolones across lipid membranes
• Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations
• Enzymatic Oxidation of Cholesterol: Properties and Functional Effects of Cholestenone in Cell Membranes
• Apolipoprotein A-I mimetic peptide 4F blocks sphingomyelinase-induced LDL aggregation.
• Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate
• Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions
• Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol
• On Atomistic Models for Molecular Oxygen
• Efficient preparation and analysis of membrane and membrane protein systems
• Molecular electrometer and binding of cations to phospholipid bilayers
• Long-chain GM1 gangliosides alter transmembrane domain registration through interdigitation
• The role of hydrophobic matching on transmembrane helix packing in cells
• Energetics of the Transmembrane Peptide Sorting by Hydrophobic Mismatch
• Diffusion Analyses along Mean and Gaussian-Curved Membranes with CurD
• A comparison of lipid diffusive dynamics in monolayers and bilayers in the context of interleaflet coupling
• Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions
• Challenges in the Accurate Modelling of Lipid Dynamics in Monolayers and Bilayers
• Lipid Scrambling Pathways in the Sec61 Translocon Complex