Variability of conformations at crystal contacts in BPTI represent true low‐energy structures: Correspondence among lattice packing and molecular dynamics structures

Abstract

The structures of five basic pancreatic trypsin inhibitor (BPTI) molecules are compared to establish the extent and nature of the conformational variability resulting from crystal packing effects. BPTI is an ideal system to evaluate such factors because of the availability of high resolution X-ray models of five different BPTI structures, each in a different crystal packing environment. Differences observed among the structures are found to be distributed throughout the molecule, although the regions that display most variability are associated with the loop structures (residues 14-17 and 24-29). The regions of structure that show the largest rms deviations from the mean of the five packing motifs correlate well with the presence of intermolecular contacts in the crystal lattice. For most of the molecules there is also a correspondence between a larger number of intermolecular contacts and systematically higher B-factors, although it is not apparent whether this is induced by the crystal contact or results from the fact that the contacts are made predominantly through surface loops. The conformational differences seen among the X-ray models constitute more than local shifts at the lattice contact surfaces, and in fact involve in some cases the making and breaking of intramolecular H-bonds. The magnitudes of the differences among packing models are significantly larger than those usually associated with changes induced by mutagenesis; for instance; the structural differences at the site of mutation observed on removing an internal disulfide from the molecule are significantly less than those associated with lattice contact effects. The crystal packing conformations are compared to representative structures of BPTI generated during a 96-psec molecular dynamics (MD) simulation. This comparison shows a high level of correspondence between the protein flexibility indicated by the X-ray and MD analyses, and specifically between those regions that are most variable. This suggests that the regions that show most variability among the crystal packing models are not artifacts of crystallization, but rather represent true low-energy conformers that have been preferentially selected by crystallization factors.

The crystal structure of the immunity protein of colicin E7 suggests a possible colicin-interacting surface.

“…Because variable loops 1 and 2 make contacts with the neighboring symmetrically related molecules, crystal packing forces may fix their conformation (18), and these two loops might have different structures in solution.…”

Crevice‐forming mutants in the rigid core of bovine pancreatic trypsin inhibitor: Crystal structures of F22A, Y23A, N43G, and F45A

“…6C,D). In addition, Kossiakoff et al (1992) have noted that this region has the most intermolecular crystallographic contacts and the most variability among the crystal structures they have compared. Main-chain coordinates at the region of residues 46-50 also have above average deviations from wild type in the F45A and F22A mutants.…”

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“…Crystal contacts are often invoked as a perturbing force to explain differences between crystal structures and solution structures, and on separate occasions have been observed to either increase or decrease the order of the affected regions (Kossiakoff et al, 1992;Young et al, 1994). The data in Figure 3 suggest that, in the case of aLP, the effect of crystal contacts on B-factors is insignificant.…”