Testing the procedure of simulated annealing by refining homologous immunoglobulin light-chain dimers

The refinement of antigen-binding fragment structures by the method of simulated annealing was tested. Using the program X-PLOR, we refined the structure of one immunoglobulin light-chain dimer against 2.8 A diffraction data collected for a homologous light-chain dimer. The refinement proceeded smoothly; alpha-carbons of the conserved segments of the domain moved to the positions in the reference structure solved independently. An average movement of approximately 1.5 A for atoms in the variable domains (half of the molecule) was observed. Though the final R-factors and energy terms of the reference and test structures were very similar, some of the chain segments of the hypervariable loops (HVR3s) and the ends of some side chains did not converge to the positions in the reference structure. Therefore, although globally the refinement worked very well, positions of the loops and the side chains that are critical for immunoglobulin function have to be carefully examined by difference Fourier techniques.