Macromolecular complexes in crystals and solutions

Abstract

This paper presents a discussion of existing methods for the analysis of macromolecular interactions and complexes in crystal packing. Typical situations and conditions where wrong answers may be obtained in the course of ordinary procedures are presented and discussed. The more general question of what the relationship is between natural (in-solvent) and crystallized assemblies is discussed and researched. A computational analysis suggests that weak interactions with K d ! 100 mM have a considerable chance of being lost during the course of crystallization. In such instances, crystal packing misrepresents macromolecular complexes and interactions. For as many as 20% of protein dimers in the PDB the likelihood of misrepresentation is estimated to be higher than 50%. Given that weak macromolecular interactions play an important role in many biochemical processes, these results suggest that a complementary noncrystallographic study should be always conducted when inferring structural aspects of weakly bound complexes.

New Insights into the Assembly of Bacterial Secretins

“…Finally, the refined model was validated using Coot (23) and MolProbity (25). The figures and structural comparisons (root mean square deviation (RMSD) calculation) were made using PyMOL (26), and analysis of dimerization interface was done using the protein interfaces, surfaces, and assemblies service of the Protein Data Bank (PDBe PISA) (27). The structure of peri-XcpQ (S210C) was determined by molecular replacement using the refined model peri-XcpQ carrying a S210A mutation as search model and was refined and validated as described above.…”

A model for non-obligate oligomer formation in protein aggregration

“…1 was predicted by PISA (available at http://www.ebi.ac.uk/pdbe/pisa/) analysis of the pdb entry 2ZKX [12]. PISA enumerates all macromolecular assemblies that may be potentially formed for a given crystal packing.…”

“…Informatics approaches that score putative protein complexes represent an attempt to enumerate possible assemblies by identifying interfaces as either biologically relevant or simply contacts due to crystal packing forces [11]. Since 2007 the PISA (Protein Interface, Surfaces and Assemblies) protocol, a graph-theoretical approach to identify chemically stable and biologically relevant associations that may potentially be formed in a given crystal packing, has been used in the PDB submission process to aid in quaternary structure determination [12]. Alternatively the user can utilize PISA to independently analyze any PDB entry.…”

Structural Biology: A Century-long Journey into an Unseen World

“…This locking of the structure is necessary for the growth of crystals that diffract to high angles and high resolution but can be problematic. In the worst cases it may give rise to misleading artefacts if molecular contacts within the crystal lattice distort the molecular structure (Krissinel 2011, Demo et al 2014. Such effects are relatively rare and should not be overstated.…”