Smith-Gill S J, Mainhart C, Lavoie T B, Feldmann R J, Drohan W, Brooks B R
Laboratory of Genetics, National Cancer Institute, Bethesda, MD 20892.
J Mol Biol. 1987 Apr 20;194(4):713-24. doi: 10.1016/0022-2836(87)90249-x.
The primary amino acid structure of the lysozyme-binding antibody, HyHEL-10, as determined by amino acid and nucleotide sequencing was utilized to construct a scale model of the Fv (variable region domain of immunoglobulin) using energy-minimized torsional angles of the McPC603 Fv as a prototype template. This model was in turn used as a template for generating a computer-built set of co-ordinates, which were subjected to a total of 600 steps of Adopted Basis Newton-Raphson energy minimizations using the program CHARMM. Only minimal shifts of the backbone (root-mean-square 0.76 A) were required to give an energetically stable structure with a favorable van der Waals' energy. Several notable features were evident from both the scale model and the energy-minimized computer model: (1) the shape of the antibody combining region is that of a very shallow concavity approximately 20 A X 25 A; (2) the concavity is acidic and non-hydrophobic and is bordered by hydrophobic segments; (3) the lower portion of the combining site is dominated by a cluster of tyrosine residues over the L3 and H2 areas; (4) a somatic mutation encoded by the J region of the heavy chain (JH) may contribute significantly to the complementarity of heavy chain H3 to the epitope on hen egg white lysozyme. In addition, the space-filling energy-minimized model revealed that residue 49L, a framework residue, was prominently exposed and accessible in the center of the combining-site concavity. The model suggests that variation in length of complementarity-determining regions may function not only to change directly the shape of the antibody combining site, but may also influence indirectly the nature of the antibody surface by changing the accessibility of residues not usually involved in antigen binding.
通过氨基酸和核苷酸测序确定的溶菌酶结合抗体HyHEL-10的一级氨基酸结构，被用于构建Fv（免疫球蛋白可变区结构域）的比例模型，该模型以McPC603 Fv的能量最小化扭转角为原型模板。这个模型反过来又被用作生成一组计算机构建坐标的模板，使用CHARMM程序对其进行了总共600步的采用基牛顿-拉夫森能量最小化。只需主链进行最小程度的移动（均方根为0.76 Å），就能得到具有良好范德华能量的能量稳定结构。从比例模型和能量最小化计算机模型中都可以明显看出几个显著特征：（1）抗体结合区域的形状是一个非常浅的凹陷，约为20 Å×25 Å；（2）凹陷呈酸性且非疏水性，周围是疏水片段；（3）结合位点的下部在L3和H2区域由一簇酪氨酸残基主导；（4）重链J区域（JH）编码的体细胞突变可能对重链H3与鸡蛋清溶菌酶表位的互补性有显著贡献。此外，填充空间的能量最小化模型显示，框架残基49L在结合位点凹陷的中心显著暴露且可及。该模型表明，互补决定区长度的变化不仅可能直接改变抗体结合位点的形状，还可能通过改变通常不参与抗原结合的残基的可及性，间接影响抗体表面的性质。
