arXiv subjects

O. H. Samuli Ollila

Publications and source records attributed to O. H. Samuli Ollila.

3 recordsLinked to original sources

arXiv2025

Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields

This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature (RT) protein crystallography. We discuss what the observables are, what they tell us about structure and dynamics, what makes them useful for assessing force field accuracy, and how they can be connected to molecular dynamics simulations carried out using the force field one wishes to benchmark. We also touch on statistical issues that arise when comparing simulations with experiment. We hope this article will be particularly useful to computational researchers and trainees who develop, benchmark, or use protein force fields for molecular simulations.

q-bio.BM↗

arXiv2021

Decoupling of dipolar and hydrophobic motions in biological membranes

Cells use homeostatic mechanisms to maintain an optimal composition of distinct types of phospholipids in cellular membranes. The hydrophilic dipolar layer at the membrane interface, composed of phospholipid headgroups, regulates the interactions between cell membranes and incoming molecules, nanoparticles, and viruses. On the other hand, the membrane hydrophobic core determines membrane thickness and forms an environment for membrane-bound molecules such as transmembrane proteins. A fundamental open question is to what extent the motions of these regions are coupled and, consequently, how strongly the interactions of lipid headgroups with other molecules depend on the properties and composition of the membrane hydrophobic core. We combine advanced solid-state nuclear magnetic resonance spectroscopy methodology with high-fidelity molecular dynamics simulations to demonstrate how the rotational dynamics of choline headgroups remain nearly unchanged (slightly faster) with incorporation of cholesterol into a phospholipid membrane, contrasting the well known extreme slowdown of the other phospholipid segments. Notably, our results suggest a new paradigm where phospholipid headgroups interact as quasi-freely rotating flexible dipoles at the interface, independent of the properties in the hydrophobic region.

cond-mat.soft↗

arXiv2015

Towards atomistic resolution structure of phosphatidylcholine glycerol backbone and choline headgroup at different ambient conditions

Phospholipids are essential building blocks of biological membranes. Despite of vast amount of accurate experimental data the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulation model would automatically resolve the structures giving an interpretation of experimental results, if the model would reproduce the experimental data. In this work we compare the C-H bond vector order parameters for glycerol backbone and choline headgroup between 14 different atomistic resolution models and experiments in fully hydrated lipid bilayer. The current models are not accurately enough to resolve the structure. However, closer inspection of three best performing models (CHARMM36, GAFFlipid and MacRog) suggest that improvements in the sampled dihedral angle distributions would potentilly lead to the model which would resolve the structure. Despite of the inaccuracy in the fully hydrated structures, the response to the dehydration, i.e. P-N vector tilting more parallel to membrane normal, is qualitatively correct in all models. The CHARMM36 and MacRog models describe the interactions between lipids and cholesterol better than Berger/Höltje model. This work has been, and continues to be, progressed and discussed through the blog: nmrlipids.blogspot.fi. Everyone is invited to join the discussion and make contributions through the blog. The manuscript will be eventually submitted to an appropriate scientific journal. Everyone who has contributed to the work through the blog will be offered coauthorship. For more details see: nmrlipids.blogspot.fi.

physics.bio-ph↗