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 Ca²⁺ 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 Ca²⁺‐guluronate with suitable lateral dimensions for crystallographic studies. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 562–571, 2013.