Conformational analysis of lipid molecules by self-organizing maps.
The authors have studied the use of the self-organizing map (SOM) in the analysis of lipid conformations produced by atomic-scale molecular dynamics simulations. First, focusing on the methodological aspects, they have systematically studied how the SOM can be employed in the analysis of lipid conformations in a controlled and reliable fashion. For this purpose, they have used a previously reported 50 ns atomistic molecular dynamics simulation of a 1-palmitoyl-2-linoeayl-sn-glycero-3-phosphatidylcholine (PLPC) lipid bilayer and analyzed separately the conformations of the headgroup and the glycerol regions, as well as the diunsaturated fatty acid chain. They have elucidated the effect of training parameters on the quality of the results, as well as the effect of the size of the SOM. It turns out that the main conformational states of each region in the molecule are easily distinguished together with a variety of other typical structural features. As a second topic, the authors applied the SOM to the PLPC data to demonstrate how it can be used in the analysis that goes beyond the standard methods commonly used to study the structure and dynamics of lipid membranes. Overall, the results suggest that the SOM method provides a relatively simple and robust tool for quickly gaining a qualitative understanding of the most important features of the conformations of the system, without a priori knowledge. It seems plausible that the insight given by the SOM could be applied to a variety of biomolecular systems and the design of coarse-grained models for these systems.
Murtola
Teemu
T
Laboratory of Physics, Helsinki University of Technology, P.O. Box 1100, FI-02015 HUT, Finland.
Kupiainen
Mikko
M
Falck
Emma
E
Vattulainen
Ilpo
I
D016000:Cluster Analysis; D003198:Computer Simulation; D008051:Lipid Bilayers / Q000737:chemistry*; D008560:Membrane Fluidity; D008968:Molecular Conformation; D010713:Phosphatidylcholines / Q000737:chemistry*; D013816:Thermodynamics
D008051:Lipid Bilayers; D010713:Phosphatidylcholines; C055402:1-palmitoyl-2-linoleoylphosphatidylcholine