M. Karttunen

Identification of Catechins Binding Pockets in Monomeric Aβ42 Through Ensemble Docking and MD Simulations

This study identifies catechins binding pockets in monomeric Aβ42 using ensemble docking and MD simulations, showing hydrophobic and hydrogen bonding interactions and potential as inhibitors against amyloid aggregation.

The structure of the enigmatic ripple phase in saturated bilayers resolved: Machine learning reveals four lipid populations

The paper uses machine learning to analyze MD simulations of DPPC bilayers and identifies four distinct lipid populations in the ripple phase.

A multiscale computational study of the conformation of the full-length intrinsically disordered protein MeCP2

This study uses computational methods to model the full-length disordered protein MeCP2, identifying two main conformations and validating the model against experimental data.

Highly similar sequence and structure yet different biophysical behaviour: A computational study of two triosephosphate isomerases

This study compares two similar TIM proteins, TcTIM and TbTIM, using MD simulations to identify biophysical differences linked to specific interactions.

Free energy and stacking of eumelaninnanoaggregates

This study investigates the structural properties of DHI eumelanin aggregates in aqueous solutions using molecular dynamics and DFT calculations, revealing non-covalent stacking and curved nanoscale domains.

Cholesterol Sequestration by Xenon Leads to Lipid Raft Destabilization

The paper uses simulations to show xenon sequesters cholesterol from lipid rafts, destabilizing them and potentially explaining xenon's anesthetic effect.

Insights into the Polyhexamethylene Biguanide (PHMB) Mechanism of Action on Bacterial Membrane and DNA: A Molecular Dynamics Study

This study uses molecular dynamics simulations to show PHMB does not form pores in bacterial membranes but instead binds to DNA, potentially blocking replication or activating repair.

Formation of aggregates, icosahedral structures and percolation clusters of fullerenes in lipids bilayers: The key role of lipid saturation

This study uses CG-MD simulations to show that lipid saturation level determines fullerene aggregation and structure formation in lipid bilayers.

Experimental and Computational Evidence for Self-Assembly of Mitochondrial UCP2 in Lipid Bilayers

This study provides experimental and computational evidence that UCP2 self-assembles into stable tetramers in lipid bilayers, which are functional for proton transport and may regulate ATP synthesis.

Phospholipid-Cellulose Interactions: Insight from Atomistic Computer Simulations for Understanding the Impact of Cellulose-Based Materials on Plasma Membranes

This study uses molecular dynamics simulations to analyze phospholipid-cellulose interactions, showing strong hydrogen bonding and structural perturbations in lipid bilayers.

Does alpha-tocopherol flip-flop help to protect membranes against oxidation?

This study uses molecular dynamics simulations to show that alpha-tocopherol flip-flop rates increase in oxidized lipid bilayers, reducing free energy barriers and enhancing membrane protection against oxidation.

The extracellular gate shapes the energy profile of an ABC exporter

This study uses a synthetic antibody to determine the structure and mechanism of an ABC exporter's extracellular gate, showing its role in ATPase activity and transport.