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New insights into the alternating sequences of heparan sulfate

Introduction  The sulfated domains (S‐domains) within HS are thought to be the primary binding site for protein ligands ( Gallagher and Lyon, 2000 ). Studies on the binding of multimeric chemokines to HS have suggested that N‐acetylated sequences (NAc‐domains) act to space the S‐domains correctly so binding can occur at more than one HS binding site within a protein ( Lortat‐Jacob et al. 1995 ; Stringer et al. 2002 ). So far, little functional significance has been ascribed to either alternating N‐sulfate/NAc or lone N‐sulfate types of sequence, although alternating sequences are thought to occur at the borders between S‐domains and NAc‐domains, forming transition zones between the two. Existing scission techniques used to excise oligosacchrides from the intact chain for structural and functional analysis disrupt the transition zones (heparinase III), or the S‐domains (heparinase I) or both (low pH nitrous acid).