Analysis of solvent content and oligomeric states in protein crystals—does symmetry matter?

Abstract

A nonredundant set of 9081 protein crystal structures in the Protein Data Bank was used to examine the solvent content, the number of polypeptide chains, and the oligomeric states of proteins in crystals as a function of crystal symmetry (as classified by crystal systems and space groups). It was found that there is a correlation between solvent content and crystal symmetry. Surprisingly, proteins crystallizing in lower symmetry systems have lower solvent content compared to those crystallizing in higher symmetry systems. Nevertheless, there is no universal correlation between solvent content and preferences of macromolecules to crystallize in certain space groups. Crystal symmetry as a function of oligomeric state was examined, where trimers, tetramers, and hexamers were found to prefer to crystallize in systems where the oligomer symmetry could be incorporated in the crystal symmetry. Our analysis also shows that the frequency distribution within the enantiomorphous pairs of space groups does not differ significantly, in contrast to previous reports.Keywords: solvent content; Matthews coefficient; protein crystals; oligomerization; space group frequency Supplemental material: see www.proteinscience.orgWater plays an important role in the structure of biomolecules and often influences protein function. Water molecules not only affect protein folding, but also mediate biological processes such as enzymatic reactions and molecular recognition. Information about the fraction of water (solvent) plays a significant role in the X-ray structure determination process. First, knowledge of the solvent content helps to determine the number of molecules in the asymmetric unit (Matthews 1968), which is crucial in early stages of crystal structure determination. Second, an approximate value of solvent content is needed for significant phase improvement by solvent flattening methods (Wang 1985;Leslie 1987;Abrahams and Leslie 1996), which is necessary to resolve the inherent phase ambiguity in single anomalous diffraction (SAD) experiments. For both SAD and MAD (multiwavelength anomalous diffraction) (Hendrickson 1991;Hendrickson et al. 1990), phase improvement by solvent flattening is critical for low resolution data (Kirillova et al. 2007), especially when non-crystallographic symmetry cannot be applied.Matthews (1968) observed that the solvent content in protein crystals ranged from 27% to 65%, with an average of 43%. He also showed that the quantity V M (the Matthews coefficient, defined as the ratio of the volume of the asymmetric unit to the molecular weight of all

Computational design of a protein crystal

“…For the crystallographic structure and this model, the computed interaction energy per protein within the P321 structure was above that of the P6 structure, i.e., the calculation did not discern P321 as the preferred crystalline structure. The observed frequency of P321, however, is more than three times the frequency of P6 (21,40). In addition, P321 can accommodate deviations from the planar layering present in P6.…”

“…Glycine and small amino acids have been suggested to promote crystallization through the reduction of surface entropy (8,14,(52)(53)(54), and the presence of GX 3 G motifs at each protein-protein interface is consistent with a tightly packed crystal. Furthermore the volume per molecular weight (Matthew's coefficient) (55 (21). The solvent content (36%) is less than that observed for typical protein crystals (51%), hexagonal protein crystals (57%), and protein crystals with four polypeptide chains in the asymmetric unit (51%) (21,55,56).…”

“…Furthermore the volume per molecular weight (Matthew's coefficient) (55 (21). The solvent content (36%) is less than that observed for typical protein crystals (51%), hexagonal protein crystals (57%), and protein crystals with four polypeptide chains in the asymmetric unit (51%) (21,55,56).…”

“…1A) offers desirable features: (i) high symmetry, which can facilitate data collection and structure determination using X-ray crystallogra-phy, (ii) tubular solvent channels extending through the crystal, and (iii) polarity, i.e., large-scale parallel orientation of the proteins. Moreover, the P6 space group is one of the less common (2), occurring in only 0.1% of known protein crystal structures (21). Thus, achieving a designed crystal with P6 ordering is a stringent test of the approach.…”

Soft matter perspective on protein crystal assembly

“…The lack of evolutionary pressure for proteins to crystallize indeed results in their crystals having most commonly the lowest-symmetry chiral (protein chains are chiral) point group compatible with that number of contacts, i.e., P2 1 2 1 2 1 [136]. Crystals of oligomeric proteins, for which evolution has shaped at least the oligomeric contacts, often assemble in complex asymmetric unit cells with more than ten distinct patches [137,138]. The competition between these interactions can favor the formation of small metastable crystallites, hindering the assembly of defectless crystals.…”