Probing the helical forms of Ca2+ -guluronan junction zones in alginate gels by molecular dynamics 1: Duplexes

A molecular dynamics investigation of the helical forms adopted by (1→4)-α-L-guluronan in explicit water environment was carried out. Single chains and duplexes were modeled at 300 K starting both from 21 or 32 helical conformations and in the presence of a neutralizing amount of Ca(2+) ions. All systems were allowed full conformational freedom. The initial perfect helices with integral screw symmetries were lost at the very beginning of simulations and two distinct behaviors were observed: At equilibrium the 21 models mostly retained the 21 local helical conformations while exploring the 32 ones the rest of the time. In duplexes the two chains, which behaved similarly, were well extended and slightly twisted. By contrast, the chains in 32 duplex models were dissimilar and explored a much broader conformational space in which 21 and 32 local helical conformations were dominant and equally represented but the 31 and other conformations were also present. The wide variety of conformations revealed in this study is consistent with the general difficulty in obtaining crystals of Ca(2+)-guluronate with suitable lateral dimensions for crystallographic studies.