Crystallographically complex

These descriptions represent somewhat idealized situations. In many real examples the modulated component of the structure can force the notionally fixed part of the structure to become modulated in turn, leading to considerable crystallographic complexity. 

Empirical Free Energy Calculations of Ligand-Protein Crystallographic Complexes. I. Knowledge-Based Ligand-Protein Interaction Potentials Applied to the Prediction of Human Immunodeficiency Virus 1 Protease Binding Affinity. 

Early reports have described species of formulation MIA OBu JM OPr1 (M = Fe,438 Ni,409 Co 439 M = Zr, Hf) although none were characterized crystallographically. Complexes containing... 

Verkhivker, G., Appelt, K., Freer, S.T., Villafranca, J.E. Empirical free eenrgy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. Protein Eng. 1995, 8, 677-91. 

Figure 7 Overlay of the ASV IN inhibitor crystallographic complex on the HIV IN crystal structure.

G. Verkhivker, K. Appelt, S. T. Freer, and J. E. Villafranca, Protein Eng., 8, 677 (1995). Empirical Free-Energy Calculations of Ligand—Protein Crystallographic Complexes. 

An optimization of the adjustable parameters Cj was obtained using the information on a set of 12 protein-protein complexes with known crystallographic structures. For this purpose, the structures of bound molecules in the crystallographic complexes where taken apart, rotated at random, and re-docked as explained. In cases where the X-ray structures of the unbound proteins are available as well, the structures of the complexes where also predicted using the atomic coordinates of the unbound molecules, completing a total of 15 test cases (see Table 1). In order to assure wild applicability of the method, a selection different protein complexes was made, which are supposed to be dominated by chemical interactions of different natures. These include several stable dimers formed between identical subunits possessing extended and specific contact surfaces, stable and specific complexes between different enzymes (endonucleases and proteases) and... 

However, if the unbound and complexed structures differ too much, the binding mode may be incorrectly predicted. The difficulty in predicting the correct interaction geometry between cytochrome c peroxidase and cytochrome c, due to the moderate extent of surface complementarity is, in fact, more evident when starting fi-om the structures of the unbound proteins, which show, respectively, 0.86 and 1.06A of r.m.s. deviation (all heavy atoms) from the corresponding conformations, in the complex. In this case, the interaction surfaces were grossly identified, but the position of cytochrome c is somewhat rotated and translated, relative to that adopted in the crystallographic complex. 

The predicted structure of a ligand-receptor complex with the better binding energy was superposed on the crystallographic complex conformation to calculate the root mean square deviation (RMSD). 

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