Mainhart C R, Potter M, Feldmann R J
Mol Immunol. 1984 Jun;21(6):469-78. doi: 10.1016/0161-5890(84)90062-2.
A refined protocol for building a hypothetical model of the J539 Fv is described. Computer programs for positioning amino acid side chains and structure energy minimization [CHARMM program of Brooks et al., J. comp. Chem. 4, 187-217 (1983)] were employed. Computer modeling was accomplished on an Evans and Sutherland picture system which permitted structure visualization in three dimensions. Peptide backbone breaksites were rejoined by monitoring for correct distances and torsion angles. A physical model was then constructed and used as a basis for further refinements such as aligning conformations around remodeled sites, adjusting proline substitutions and optimizing hydrogen-bond-forming potentials. This structure (J539-ADO) was energy minimized and the final coordinates were obtained from the energy-refined model. The resulting hypothetical J539 structure can be compared to the structure of J539 now being determined by X-ray crystallography. The procedures described can be used for other Fv fragments.
本文描述了构建J539 Fv假设模型的优化方案。使用了用于定位氨基酸侧链和结构能量最小化的计算机程序[Brooks等人的CHARMM程序，《计算化学杂志》4，187 - 217（1983）]。计算机建模是在Evans和Sutherland图像系统上完成的，该系统允许三维结构可视化。通过监测正确的距离和扭转角来重新连接肽主链断裂位点。然后构建一个物理模型，并将其用作进一步优化的基础，例如围绕重塑位点对齐构象、调整脯氨酸取代以及优化氢键形成潜力。对该结构（J539 - ADO）进行能量最小化，并从能量优化模型中获得最终坐标。所得的假设J539结构可与目前通过X射线晶体学确定的J539结构进行比较。所描述的程序可用于其他Fv片段。
