Principles and characteristics of biological assemblies in experimentally determined protein structures. (April 2019)

• Record Type: Journal Article
• Authors: Xu, Qifang; Dunbrack, Roland L
• Is Part Of: Current opinion in structural biology. Volume 55(2019)
• Page Start: 34
• Page End: 49
• Publication Date: 2019-04
• Subjects: Molecular biology -- Periodicals; 570
• DOI: 10.1016/j.sbi.2019.03.006
• Languages: English
• ISSNs: 0959-440X

Abstract

Highlights: Biological assemblies are the most biologically relevant structures present in experimentally determined protein structures. They can be defined by their stoichiometry, symmetry, and the protein-protein interfaces present in an assembly. In crystal structures, these assemblies must be distinguished from crystal contacts. Benchmarking is challenging since most assembly structures are known from crystals, leading to circular reasoning. Recent successful methods for identifying assemblies depend on comparison of multiple crystal forms across protein families. Abstract : More than half of all structures in the PDB are assemblies of two or more proteins, including both homooligomers and heterooligomers. Structural information on these assemblies comes from X-ray crystallography, NMR, and cryo-EM spectroscopy. The correct assembly in an X-ray structure is often ambiguous, and computational methods have been developed to identify the most likely biologically relevant assembly based on physical properties of assemblies and sequence conservation in interfaces. Taking advantage of the large number of structures now available, some of the most recent methods have relied on similarity of interfaces and assemblies across structures of homologous proteins.