Computational tools in protein crystallography

Emerging Topics in Protein Crystallography

Protein crystallography is the discipline concerned with the determination of the three-dimensional structure of biological macromolecules in a crystalline state [...].

Copper-based pulsed dipolar ESR spectroscopy as a probe of protein conformation linked to disease states

We demonstrate the ability of pulsed dipolar electron spin resonance (ESR) spectroscopy (PDS) to report on the conformation of Cu-Zn superoxide dismutase (SOD1) through the sensitive measurement of dipolar interactions between inherent Cu(2+) ions. Although the extent and the anisotropy of the Cu ESR spectrum provides challenges for PDS, Ku-band (17.3 GHz) double electron-electron resonance and double-quantum coherence variants of PDS coupled with distance reconstruction methods recover Cu-Cu distances in good agreement with crystal structures. Moreover, Cu-PDS measurements expose distinct differences between the conformational properties of wild-type SOD1 and a single-residue variant (I149T) that leads to the disease amyotrophic lateral sclerosis (ALS). The I149T protein displays a broader Cu-Cu distance distribution within the SOD1 dimer compared to wild-type. In a nitroxide (NO)-labeled sample, distance distributions obtained from Cu-Cu, Cu-NO, and NO-NO separations reveal increased structural heterogeneity within the protein and a tendency for mutant dimers to associate. In contrast, perturbations caused by the ALS mutation are completely masked in the crystal structure of I149T. Thus, PDS readily detects alterations in metalloenzyme solution properties not easily deciphered by other methods and in doing so supports the notion that increased range of motion and associations of SOD1 ALS variants contribute to disease progression.

Determination of antibody structures

While antibodies share a conserved structural framework, their complementarity-determining region loops are highly variable in size and sequence. Even more variable are the potential ways these loops can be used to interact with antigen. Thus, X-ray crystal structures of antibody Fab fragments and Fab-antigen complexes are critical for a detailed understanding of the antibody-antigen recognition process. This chapter describes the basic procedures necessary for the crystallization and structure determination of antibody Fab fragments by X-ray crystallography.