Wright C S, Kellogg G E
Department of Biochemistry and Molecular Biophysics, Medical College of Virginia, Virginia Commonwealth University, Richmond 23298, USA.
Protein Sci. 1996 Aug;5(8):1466-76. doi: 10.1002/pro.5560050803.
The binding interactions of N-acetyl-D-neuraminic acid and N,N' diacetyl-chitobiose (GlcNAc-beta-1,4-GlcNAc), observed in crystal complexes of wheat germ agglutinin (WGA) at four independent sites/monomer, were analyzed and compared with the modeling program HINT (Hydropathic INTeractions). This empirical method allows assessment of relative ligand binding strength and is particularly applicable to cases of weak binding where experimental data is absent. Although the four WGA binding sites are interrelated by a fourfold sequence repeat (eight sites/dimer), similarity extends only to the presence of an aromatic amino acid-rich pocket and a conserved serine. Strong binding requires additional interactions from a contacting domain in the second subunit. Ligand positions were either derived from crystal structures and further optimized by modeling and molecular mechanics, or from comparative modeling. Analysis of the overall HINT binding scores for the two types of ligands are consistent with the presence of two high-affinity and two low-affinity sites per monomer. Identity of these sites correlates well with crystal structure occupancies. The high-affinity sites are roughly equivalent, as predicted from solution binding studies. Binding scores for the low-affinity sites are weaker by at least a factor of two. Quantitative estimates for polar, nonpolar, and ionic interactions revealed that H-bonding makes the largest contribution to complex stabilization in the seven bound configurations, consistent with published thermodynamic data. Although the observed nonpolar interactions are small, they may play a critical role in orienting the ligand optimally.
在小麦胚凝集素（WGA）的晶体复合物中，于四个独立位点/单体观察到的N-乙酰-D-神经氨酸与N,N'-二乙酰壳二糖（GlcNAc-β-1,4-GlcNAc）的结合相互作用，被进行了分析，并与建模程序HINT（亲水性相互作用）进行了比较。这种经验方法能够评估相对配体结合强度，特别适用于缺乏实验数据的弱结合情况。尽管四个WGA结合位点通过四重序列重复相互关联（八个位点/二聚体），但相似性仅延伸至富含芳香族氨基酸的口袋和一个保守丝氨酸的存在。强结合需要来自第二个亚基中接触结构域的额外相互作用。配体位置要么源自晶体结构，并通过建模和分子力学进一步优化，要么源自比较建模。对两种类型配体的整体HINT结合分数的分析与每个单体存在两个高亲和力位点和两个低亲和力位点相一致。这些位点的身份与晶体结构占有率密切相关。如溶液结合研究预测的那样，高亲和力位点大致相当。低亲和力位点的结合分数至少弱两倍。对极性、非极性和离子相互作用的定量估计表明，在七种结合构型中，氢键对复合物稳定性的贡献最大，这与已发表的热力学数据一致。尽管观察到的非极性相互作用较小，但它们可能在最佳定向配体方面起关键作用。
