Some 10% of the antithrombin fromnormal human plasma can be isolated onthe basis of its higher affinity forheparin Sepharose. Not only does this ATIII beta have a higher heparinaffinity, but it is also less negatively charged and has a lower molecular weight than normal AT-III alpha.Neuraminidase and Endo F treatment suggest the loss of a single carbohydrate sidechain from beta AT-III (Peterson and Blackburn. J Biol Chem 1985,260, 610)Antithrombin has a single polypeptide chain with biantennary carbohydrate attachment sites at asparagines 96, 135, 155 and 172. The 25 kDA CNBr fragment of AT-III alpha (residues 104-251) runs at 22.5kDa in the case of AT-III beta yet they have the same N and C-terminal sequence. Tryptic peptide maps of theseCNBr fragments showed that a single neutral (glyco) peptide, Lys-Ala-Asn⋆-Lys was missing from AT-III beta and replaced by twobasic peptides, Lys, Ala, Asn, Lys and Ala, Asn, Lys; indicating the absence of an oligosaccharide sidechainon asparagine 135. This was confirmed by chromatography of tryptic peptides on Con A-Sepharose followed by mapping of the bound and unbound fractions. There were two new unbound peptides (Lys, Ala, Asn, Lys and Ala, Asn, Lys) in AT-III beta. The corresponding peptide Lys-Ala-Asn⋆-Lys was the only peptide missing from the bound glycopeptide fraction.The absence of carbohydrate at Asn 135 explains the increased heparinaffinity of beta AT-III as on the molecular model this oligosaccharide forms a negative and bulky shell on the perimeter of the positive bindingsite centred on Arg 47.Whether the loss of the sidechain is due to circulatory removal is not known but a recent variant identification confirmsthat it may alternatively be due to failure of attachment at the time ofsynthesis. Potentially the loss or modification of oligosaccharide 135 provides another level of control of coagulation by altering the avidity of AT-III for thrombin when heparin activation is suboptimal.