Indian Journal of Biochemistry & Biophysics Vo!. 39, April 2002, pp. 87-92 Conformation, orientation and dynamics of dodecylphosphocholine in micellar aggregate: A 3.2 ns molecular dynamics simulation study Sheeja V Vasudevan and Petety V Balaji* Biotechnology Center, Indian Institute of Technology, Bombay, Powai, Mumbai 400076, India Received ]0 September 200]; revised and accepted 26 December 200] A dodecylphosphocholine micelle of 86 monomers with 5776 water molecules has been simulated under NPT conditions for 3.2 ns using GROMACS2.0. The micelle was found to be very dynamic. Some of the C-C bonds, independent of their position in the DPC monomer, adopt gauche conformation and the trans H gauche transitions are quite frequent. An average of about II % of the C-C bonds in the micelle are observed to be in the gauche conformation (i.e., Idihedral angle 1< 120°). The terminal methyl groups are randomly distributed all over the micelle whereas the nitrogen atom of phosphocholine headgroup atoms is restricted to the interface region. Some of the monomers were found to lie on the surface. The shape of micelle, influenced by the packing considerations, shows deviations from spherical shape. The phosphocholine headgroup is well solvated and there is no water penetration into the micelle core. The overall features of the micelle of 86 DPC monomers conforms to the lattice model of micelle proposed by Dill and Flory [Dill K A, Flory P J (1981) Proc Natl Acad Sci USA 78, 676-680] and is similar to DPC micelles of smaller aggregate sizes except for the positional preference of the C-C bonds for the gauche conformation and the trans ...... gauche transition times [Tieleman D P, van der Spoel D, Berendsen H J C (2000) J Phys Chem B 104,6380-6388; Wymore T, Gao X F, Wong T C (1999) J Mol Slrucf (Theochem) 485-486, 195-210]. It appears that packing considerations play a predominant role in determining the shape and dynamics of the micelle. Micelles, especially those of dodecylphosphocholine (OPC), are being increasingly used as model systems to mimic bilayers in various experimental studies I. This, together with improvements in methodology and computational resources, has led to an increasing number of molecular dynamics (MD) simulations to address issues related to the dynamic properties of lipid aggregates in aqueous media 2 - 6 . Recently, MD simulation studies on the structure and dynamics of ope micelles of varying aggregation sizes have been reported 7 ,8, In these studies, a DPe micelle of 54 monomers was simulated for 15.4 ns (referred to as M54 simulation henceforth)7; the length of the simulation for the other three aggregate sizes is 1,06 ns for micelles of 40 and 65 monomers (M40 and M65 simulations)7 and 1.2 ns for the micelle of 60 monomers (M60 simulation)8. A recent MD study of octylglucoside micelles of different aggregate sizes showed that the structural aspects of the micelles are strongly influenced by the structure of the amphiphile 9 . It was also observed from this MD study on octylglucoside micelles that the accessible surface * Author for correspondence Tel.: +91-22-576 7778; Fax: 572 3480 E-mail: balaji@btc.iitb.ac.in area (ASA) per lipid decreases with an increase in the aggregate size; in particular, the ASA for the hydrocarbon tail in the micelle of 75 monomers (largest aggregate size simulated by Bogusz et al.) was very close to the corresponding value for a bilayer9. The aggregation number of micelle has been shown to be influenced by impurities, temperature, nature and length of hydrocarbon chains, nature of the headgroup, salt concentration and the association of other molecules 1,10-14. It has also been suggested that micelles do not have one definite size but comprise a large range of aggregation numbers with a concentration maximum around a mean aggregation number 1o ,13. Although the aggregation number for pure oep micelles has been found to be 56±5 at 20 0 e l I, for dedecyl detergent micelles in general, the aggregation number has been observed to range from SO to 90 at 25°e 1o . In this background, the present MD simulation study was undertaken to investigate, in atomic detail, the structure and dynamics of ope micelle containing 86 monomers in presence of explicit water molecules. The results from the 3.2 ns MD study show that the overall dynamic features and the orientation and shape of the 86-monomers micelle is very similar to those of smaller aggregate size ope