Application of self-organizing maps in conformational analysis of lipids.
The characteristics of lipid assemblies are important for the functions of biological membranes. This has led to an increasing utilization of molecular dynamics simulations for the elucidation of the structural features of biomembranes. We have applied the self-organizing map (SOM) to the analysis of the complex conformational data from a 1-ns molecular dynamics simulation of PLPC phospholipids in a membrane assembly. Mapping of 1.44 million molecular conformations to a two-dimensional array of neurons revealed, without human intervention, the main conformational features in hours. Both the whole molecule and the characteristics of the unsaturated fatty acid chains were analyzed. All major structural features were easily distinguished, such as the orientational variability of the headgroup, the mainly trans state dihedral angles of the sn-1 chain, and both straight and bent conformations of the unsaturated sn-2 chain. Furthermore, presentation of the trajectory of an individual lipid molecule on the map provides information on conformational dynamics. The present results suggest that the SOM method provides a powerful tool for routinely gaining rapid insight to the main molecular conformations as well as to the conformational dynamics of any simulated molecular assembly without the requirement of a priori knowledge.
Hyvönen
M T
MT
Contribution from the Wihuri Research Institute, Kalliolinnantie 4, FIN-00140 Helsinki, Finland. Marja-Hyvonen@wri.fi
Hiltunen
Y
Y
El-Deredy
W
W
Ojala
T
T
Vaara
J
J
Kovanen
P T
PT
Ala-Korpela
M
M
D008051:Lipid Bilayers; D008958:Models, Molecular; D008968:Molecular Conformation; D010713:Phosphatidylcholines / Q000737:chemistry*
D008051:Lipid Bilayers; D010713:Phosphatidylcholines; C055402:1-palmitoyl-2-linoleoylphosphatidylcholine