Disordered biomolecules

We combine NMR experiments and MD simulations to study biomolecules without well-defined structure, like intrinsically disordered proteins and lipids. Topics range from understanding the mesoscopic structure of biomaterials to complicated biophysical processes. We also improve force fields and develop methods to interpret NMR experiments by using MD simulations. 

Heterogeneous dynamics in partially disordered proteins Phys. Chem. Chem. Phys., 22, 21185-21196 (2020)
Improved Cation Binding to Lipid Bilayer with Negatively Charged POPS by Effective Inclusion of Electronic Polarization J. Chem. Theory Comp., 16, 738-748 (2020)
Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations J. Phys. Chem. B, 122, 6559-6569 (2018)
Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization J. Phys. Chem. B, 122, 4546-4557 (2018)
Acyl chain disorder and azelaoyl orientation in lipid membranes containing oxidized lipids Langmuir, 32, 6524 (2016)
Model-free estimation of the effective correlation time for C-H bond reorientation in amphiphilic bilayers: 1H-13C solid-state NMR and MD simulations J Chem. Phys., 142, 044905 (2015)
Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studied with 1H-13C solid-state NMR and molecular dynamics simulations Langmuir, 30, 461-469 (2014)

Novel methods for scientific collaboration

We explore novel tools for scientific communication in the NMRlipids project. The goal is to find classical MD simulation models that correctly describe lipid structures and ion binding in model cell membranes using open collaboration. The data collected in the project is also indexed as a databank of biomolecular MD simulations in

Using open data to rapidly benchmark biomolecular simulations: Phospholipid conformational dynamics J. Chem. Inf. Model., 61, 938-949 (2021)
Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers J. Phys. Chem. B, 123, 9066-9079 (2019)
Molecular electrometer and binding of cations to phospholipid bilayers Phys. Chem. Chem. Phys., 18, 32560 (2016)
Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments BBA - Biomembranes, 1858, 2512 (2016)
Toward atomistic resolution structure of phosphatidylcholine headgroup and glycerol backbone at different ambient conditions J. Phys. Chem. B, 119, 15075 (2015)

Local pressure and tension in biological interfaces

Classical descriptions of interfacial energies with tension and bending terms are often too simplistic for biological interfaces, like lipid bilayers and monolayers. Local pressure description is an intermediate between atomistic and continuum levels. While local pressures from lipid layers have not been yet measured directly, the robustness and physical relevance of pressure profiles calculated from atomistic or coarse-grained simulations is actively debated. We aim to connect the local pressure profiles calculated from simulations to direct experimental observables to clarify the role of local pressure in biophysical processes. 

Atomistic Model for Near-Quantitative Simulations of Langmuir Monolayers Langmuir, 34, 2565-2572 (2018)
Can pyrene probes be used to measure lateral pressure proles of lipid membranes? Perspective through atomistic simulations (BBA) - Biomembranes, 1838, 1406-1411 (2014)
Interfacial Tension and Surface Pressure of High Density Lipoprotein, Low Density Lipoprotein, and Related Lipid Droplets Biophys. J. 103, 1236-1244 (2012)
Protein shape change has a major effect on the gating energy of a mechanosensitive channel Biophys. J., 100, 1651-1659 (2011)
Lateral pressure profiles in Lipid Membranes: Dependence on molecular composition in Molecular Simulations and Biomembranes: From Biophysics to Function edited by M. Sansom and P. Biggin, Royal Society of Chemistry (2010)
Membrane simulations mimicking acidic pH reveal increased thickness and negative curvature in a bilayer consisting of lysophosphatidylcholines and free fatty acids BBA - Biomembranes, 1798, 938-946 (2010)
3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes Phys. Rev. Lett. 102,078101 (2009)
Lateral pressure in lipid membranes and its role in function of membrane proteins, O. H. Samuli Ollila, Ph.D. Thesis (2010)