The structure of the trigonal crystal form of bovine b-lactoglobulin variant B at pH 7.1 has been determined by X-ray diffraction methods at a resolution of 2.22 Å and refined to values for R and R free of 0.239 and 0.286, respectively. By comparison with the structure of the trigonal crystal form of bovine b-lactoglobulin variant A at pH 7.1, which was determined previously @Qin BY et al., 1998, Biochemistry 37:14014-14023#, the structural consequences of the sequence differences D64G and V118A of variants A and B, respectively, have been investigated. Only minor differences in the core calyx structure occur. In the vicinity of the mutation site D64G on loop CD~residues 61-67!, there are small changes in main-chain conformation, whereas the substitution V118A on b-strand H is unaccompanied by changes in the surrounding structure, thereby creating a void volume and weakened hydrophobic interactions with a consequent loss of thermal stability relative to variant A. A conformational difference is found for the loop EF, implicated in the pH-dependent conformational change known as the Tanford transition, but it is not clear whether this reflects differences intrinsic to the variants in solution or differences in crystallization.Keywords: bovine b-lactoglobulin; crystal structure; genetic variants; hydrophobic stabilization Bovine b-lactoglobulin~BLG!, the major whey protein of cow's milk at a concentration of 0.3 g0100 mL~Bell & McKenzie, 1964!, was first isolated by Palmer~1934!. Mature bovine b-lactoglobulin has 162 residues, and is a member of the lipocalin protein superfamily~Flower, 1994, 1996!. Members of this family have a distinctive eight-stranded b-barrel structure, the central cavity of which binds a variety of hydrophobic molecules~Banaszak et al., 1994!. In the case of BLG, the primary site for fatty-acid binding has recently been established crystallographically to be inside this cavity~Qin et al., 1998b; Wu et al., 1999!. The structure of BLG is now reliably known following two independent redeterminations of the structure in the triclinic~lattice X!~Brownlow et al., 1997! and orthorhombic~lattice Y! forms~Bewley et al., 1997!. The latter structure has led to our redetermination of the structure in the trigonal~lattice Z! form~Qin et al., 1998a!. In lattice Z, in contrast to lattices X and Y, the entire molecule is well defined from electron density maps.Three variants of BLG, labeled as A, B, and C, commonly occur in cow's milk. Variants A and B~BLGA and BLGB! differ at two sites: Asp64 in A is changed to Gly in B, and Val118 in A is changed to Ala in B. Variants B and C differ at one site: Gln59 in B is changed to His in C. Thus, the isoelectric points for variants A, B, and C differ slightly: pI ϭ 5.26, 5.34, and 5.33, respectively, in 0.1 M KCl at room temperature~McKenzie, 1971!. Of technological significance, bovine BLG variants have different effects on the industrial processing of milk and on the characteristics of milk products~Hill et al., 1996!. Thermal stability is in the order B ...