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Probing the helical forms of Ca 2+ ‐guluronan junction zones in alginate gels by molecular dynamics 1: Duplexes
Author(s) -
Wolnik Anna,
Albertin Luca,
Charlier Landry,
Mazeau Karim
Publication year - 2013
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.22216
Subject(s) - chemistry , molecular dynamics , duplex (building) , crystallography , helix (gastropod) , ion , stereochemistry , computational chemistry , dna , ecology , biochemistry , organic chemistry , snail , biology
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.