Probing the helical forms of Ca 2+ ‐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 2 1 or 3 2 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 2 1 models mostly retained the 2 1 local helical conformations while exploring the 3 2 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 3 2 duplex models were dissimilar and explored a much broader conformational space in which 2 1 and 3 2 local helical conformations were dominant and equally represented but the 3 1 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. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 562–571, 2013.