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List of works by Ilpo Vattulainen

A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction.

scientific article

An efficient auxin-inducible degron system with low basal degradation in human cells

scientific article published on 26 August 2019

Antidepressant drugs act by directly binding to TRKB neurotrophin receptors

scientific article published on 18 February 2021

Apolipoprotein A-I mimetic peptide 4F blocks sphingomyelinase-induced LDL aggregation

scientific article published on 10 April 2015

Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling

scientific article published on 10 September 2018

Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers

scientific article published on 25 September 2017

Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis

scientific article published on 16 February 2017

Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex

scientific article published on 26 September 2016

Atomistic fingerprint of hyaluronan-CD44 binding

scientific article published on 17 July 2017

Author Correction: An efficient auxin-inducible degron system with low basal degradation in human cells

scientific article published on 01 November 2019

BODIPY-cholesterol: a new tool to visualize sterol trafficking in living cells and organisms

scientific article published on 19 July 2008

Biogenesis of Nascent High Density Lipoprotein Particles

scientific article published on 01 July 2015

Bobbing of Oxysterols: Molecular Mechanism for Translocation of Tail-Oxidized Sterols through Biological Membranes.

scientific article published on 13 February 2018

Calcium Assists Dopamine Release by Preventing Aggregation on the Inner Leaflet of Presynaptic Vesicles

scientific article published on 6 February 2017

Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition

scientific article published on 08 February 2017

Ceramide-1-phosphate, in contrast to ceramide, is not segregated into lateral lipid domains in phosphatidylcholine bilayers

scientific article published on March 2009

Cholesterol Modulated Interdigitation of Long-Chain Sphingomyelin and Glycolipids

Cholesterol Protects the Oxidized Lipid Bilayer from Water Injury: An All-Atom Molecular Dynamics Study

scientific article published on 17 March 2018

Cholesterol oxidation products and their biological importance

scientific article published on 5 March 2016

Cholesterol under oxidative stress—How lipid membranes sense oxidation as cholesterol is being replaced by oxysterols

scientific article published on 17 March 2015

Co-exposure with fullerene may strengthen health effects of organic industrial chemicals

scientific article

Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints

article

Comparison of cholesterol and its direct precursors along the biosynthetic pathway: effects of cholesterol, desmosterol and 7-dehydrocholesterol on saturated and unsaturated lipid bilayers

scientific article

Composition and lipid spatial distribution of HDL particles in subjects with low and high HDL-cholesterol

scientific article

Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin

scientific article published on 30 October 2017

Conformational analysis of lipid molecules by self-organizing maps

scientific article published on 01 February 2007

Cryo-EM structure of the complete and ligand-saturated insulin receptor ectodomain

scientific article published on 01 January 2020

Cryo-EM, X-ray diffraction, and atomistic simulations reveal determinants for the formation of a supramolecular myelin-like proteolipid lattice

scientific article published on 07 April 2020

Crystalline Wax Esters Regulate the Evaporation Resistance of Tear Film Lipid Layers Associated with Dry Eye Syndrome

scientific article published on 01 July 2019

Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters

scientific article

Diffusion of Integral Membrane Proteins in Protein-Rich Membranes

scientific article published on 19 August 2017

Distribution and dynamics of quinones in the lipid bilayer mimicking the inner membrane of mitochondria

scientific article published on 21 June 2016

Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle

scientific article published on 17 July 2017

Dynamics of the Peripheral Membrane Protein P2 from Human Myelin Measured by Neutron Scattering--A Comparison between Wild-Type Protein and a Hinge Mutant

scientific article

Effects of DPH on DPPC-cholesterol membranes with varying concentrations of cholesterol: from local perturbations to limitations in fluorescence anisotropy experiments

scientific article published in March 2010

Effects of Membrane PEGylation on Entry and Location of Antifungal Drug Itraconazole and Their Pharmacological Implications

scientific article published on 24 February 2017

Excessive aggregation of membrane proteins in the Martini model

scientific article

Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate

scientific article published on 25 October 2014

Glucosylceramide modifies the LPS-induced inflammatory response in macrophages and the orientation of the LPS/TLR4 complex in silico

scientific article published in Scientific Reports

Glycolipid membranes through atomistic simulations: effect of glucose and galactose head groups on lipid bilayer properties.

scientific article published on 3 August 2007

Glycosylation Affects the Conformational Behavior of EGFR

Glycosylation and Lipids Working in Concert Direct CD2 Ectodomain Orientation and Presentation

scientific article

How Cardiolipin Peroxidation Alters the Properties of the Inner Mitochondrial Membrane?

scientific article published on 30 April 2018

How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: β₂-Adrenergic Receptor in the Spotlight.

scientific article

How Well Does BODIPY-Cholesteryl Ester Mimic Unlabeled Cholesteryl Esters in High Density Lipoprotein Particles?

scientific article published on 17 December 2015

How endoglucanase enzymes act on cellulose nanofibrils: role of amorphous regions revealed by atomistic simulations

How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative

scientific article published on 18 July 2018

Influence of DPH on the structure and dynamics of a DPPC bilayer

scientific article

Influence of Pyrene-Labeling on Fluid Lipid Membranes

scientific article published on 01 August 2006

Influence of cis double-bond parametrization on lipid membrane properties: how seemingly insignificant details in force-field change even qualitative trends

scientific article

Interaction of fusidic acid with lipid membranes: Implications to the mechanism of antibiotic activity

scientific article published on 16 June 2006

Interdigitation of long-chain sphingomyelin induces coupling of membrane leaflets in a cholesterol dependent manner

scientific article published on 2 December 2015

Key steps in unconventional secretion of fibroblast growth factor 2 reconstituted with purified components.

scientific article published on 19 July 2017

Lateral Diffusion in Lipid Membranes through Collective Flows

article

Lipid domain morphologies in phosphatidylcholine-ceramide monolayers

scientific article published in April 2009

Lipid membranes: Theory and simulations bridged to experiments

scientific article published on 14 June 2016

Lipids, Neurotransmitters and their Receptors

scholarly article by Hanna Juhola et al published February 2017 in Biophysical Journal

Long-chain GM1 gangliosides alter transmembrane domain registration through interdigitation

scientific article published on 28 January 2017

Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

scientific article

Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations

scientific article published on 07 February 2020

Mechanism of synergistic actin filament pointed end depolymerization by cyclase-associated protein and cofilin

scientific article published on 22 November 2019

Mechanistic principles underlying regulation of the actin cytoskeleton by phosphoinositides

scientific article

Membrane-Dependent Binding and Entry Mechanism of Dopamine into Its Receptor

scientific article published on 15 June 2020

Microscopic Mechanism for Cold Denaturation

scientific article published in Physical Review Letters

Molecular Basis of GLUT4 in Glucose Transport: Atomistic Molecular Dynamics Study

Molecular dynamics study of charged dendrimers in salt-free solution: Effect of counterions

article

Molecular mechanism for inhibition of twinfilin by phosphoinositides

scientific article published on 7 February 2018

Molecular mechanisms of Charcot-Marie-Tooth neuropathy linked to mutations in human myelin protein P2.

scientific article published on 26 July 2017

Molecular organization of the tear fluid lipid layer

scientific article published on October 2010

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

scientific article published on 12 March 2019

Multiscale modeling of emergent materials: biological and soft matter

scientific article published on 25 February 2009

Mutually Exclusive Roles of SHARPIN in Integrin Inactivation and NF-κB Signaling

scientific article published on 23 November 2015

N-Glycosylation as determinant of epidermal growth factor receptor conformation in membranes

scientific article

Nanoscale Membrane Domain Formation Driven by Cholesterol.

scientific article

Negatively Charged Gangliosides Promote Membrane Association of Amphipathic Neurotransmitters

scientific article published on 01 June 2018

Nonequilibrium effects in diffusion of interacting particles on vicinal surfaces

scientific article published on 01 June 2005

On Atomistic Models for Molecular Oxygen

scientific article published on 22 December 2016

Oxidation of Cholesterol Changes the Permeability of Lipid Membranes

Oxidation of Cholesterol Does Not Alter Significantly Its Uptake into High-Density Lipoprotein Particles

scientific article published on 24 March 2015

PEGylated Liposomes as Carriers of Hydrophobic Porphyrins

article published in 2015

PI(4,5)P 2 Binds to Phospholipase C Delta 1 in a Cholesterol Concentration Dependent Manner: Perspective on Implications to PI(4,5)P 2 -Binding Proteins

PIP2 and Talin Join Forces to Activate Integrin

article

Phase Partitioning of GM1 and Its Bodipy-Labeled Analog Determine Their Different Binding to Cholera Toxin

scientific article published on 9 May 2017

Properties of the Membrane Binding Component of Catechol-O-methyltransferase Revealed by Atomistic Molecular Dynamics Simulations

article

Protein Crowding in Lipid Bilayers Gives Rise to Non-Gaussian Anomalous Lateral Diffusion of Phospholipids and Proteins

Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase

scientific article

Quantitative Assessment of Methods Used To Obtain Rate Constants from Molecular Dynamics Simulations—Translocation of Cholesterol across Lipid Bilayers

scientific article published on 19 June 2018

Redox-coupled quinone dynamics in the respiratory complex I

article published in the Proceedings of the National Academy of Sciences of the United States of America

Redox-induced activation of the proton pump in the respiratory complex I.

scientific article

Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions

scientific article published on 20 May 2019

Reptational dynamics in dissipative particle dynamics simulations of polymer melts

article

Role of charged lipids in membrane structures - Insight given by simulations

scientific article

Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase

scientific article published on 17 April 2015

Sec14-nodulin proteins and the patterning of phosphoinositide landmarks for developmental control of membrane morphogenesis

scientific article published on 4 March 2015

Seipin traps triacylglycerols to facilitate their nanoscale clustering in the endoplasmic reticulum membrane

scientific article published on 22 January 2021

Selective effect of cell membrane on synaptic neurotransmission

scientific article

Significance of sterol structural specificity. Desmosterol cannot replace cholesterol in lipid rafts

scientific article

Structural basis of actin monomer re-charging by cyclase-associated protein.

scientific article

Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins.

scientific article

Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer

scientific article published on August 2009

Tail-Oxidized Cholesterol Enhances Membrane Permeability for Small Solutes

scientific article published on 17 August 2020

Temperature-induced structural transition in-situ in porcine lens--changes observed in void size distribution

scientific article published in February 2010

The Devil Is in the Details: What Do We Really Track in Single-Particle Tracking Experiments of Diffusion in Biological Membranes?

scientific article published on 19 February 2019

The Effect of Membrane Polyunsaturated Fatty Acids on Receptor Partitioning to Ordered Domains

The F1 loop of the talin head domain acts as a gatekeeper in integrin activation and clustering

scientific article published on 12 October 2020

The Integrin Receptor in Biologically Relevant Bilayers: Insights from Molecular Dynamics Simulations. ⬇️

scientific article published on 27 July 2016

The Na,K-ATPase acts upstream of phosphoinositide PI(4,5)P2 facilitating unconventional secretion of Fibroblast Growth Factor 2

scientific article published on 25 March 2020

The Role of Temperature and Lipid Charge on Intake/Uptake of Cationic Gold Nanoparticles into Lipid Bilayers

scientific article published on 23 April 2019

The role of hydrophobic matching on transmembrane helix packing in cells

scientific article published on 02 November 2017

Transient Ordered Domains in Single-Component Phospholipid Bilayers

scientific article published in Physical Review Letters

Under the influence of alcohol: the effect of ethanol and methanol on lipid bilayers

scientific article published on 2 December 2005

Understanding the Role of Lipids in Signaling Through Atomistic and Multiscale Simulations of Cell Membranes

scientific article published on 01 May 2019

What Can We Learn about Cholesterol's Transmembrane Distribution Based on Cholesterol-Induced Changes in Membrane Dipole Potential?

scientific article

doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS.

scientific article published on 14 September 2017

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