Paper Citing NAMD - Abstract
Wei, Chenyu; Pohorile, Andrew
Permeation of Nucleosides through Lipid Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 115:3681-3688, APR 7 2011
Elucidating mechanisms that facilitate primordial synthesis of information polymers is central to understanding the origins of life. One such mechanism might have been the recently discovered diastereoselectivity of membranes favoring uptake of ribose (Sacerdote, M. G.; Szostak, J. W. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6004), which might have promoted its preferential incorporation into nucleic acids. To determine whether the same mechanism was available if nucleosides rather than sugars were supplied to ancestral cells, we carry out molecular dynamics simulations of their permeation through a lipid bilayer. We find that the free energy barriers to permeation of ribo-adenosine and arabino-adenosine through the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine membrane are quite similar, equal to 10.0 and 10.4 kcal/mol, respectively. The corresponding permeability coefficients are also similar, equal to 9.1 x 10(-7) and 5.3 x 10(-7) cm/s. The 10-fold increase in permeability of membranes to ribose over its diastereomers is not preserved for nucleosides because in contrast to free aldopentoses they exist in the furanose rather than pyranose form. This change eliminates the possibility of forming a network of favorable, intramolecular interactions between exocyclic, hydroxyl groups that stabilizes ribose, but not its diastereomers, inside membranes. Thus, uptake of nutrients provided selective advantage to primordial RNA only if the species absorbed through cell walls were sugars rather than nucleosides.
