Application of Self-Organizing Maps in Conformational Analysis of Lipids

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• 作者：Marja T. Hyvö ; nen ; Yrjö ; Hiltunen ; Wael El-Deredy ; Timo Ojala ; Juha Vaara ; Petri T. Kovanen ; and Mika Ala-Korpela
• 刊名：Journal of the American Chemical Society
• 出版年：2001
• 出版时间：February 7, 2001
• 年：2001
• 卷：123
• 期：5
• 页码：810 - 816
• 全文大小：575K
• 年卷期：v.123,no.5(February 7, 2001)
• ISSN：1520-5126

文摘

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 structuralfeatures of biomembranes. We have applied the self-organizing map (SOM) to the analysis of the complexconformational 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, withouthuman intervention, the main conformational features in hours. Both the whole molecule and the characteristicsof 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 trajectoryof an individual lipid molecule on the map provides information on conformational dynamics. The presentresults suggest that the SOM method provides a powerful tool for routinely gaining rapid insight to the mainmolecular conformations as well as to the conformational dynamics of any simulated molecular assemblywithout the requirement of a priori knowledge.