Abstract
Proteomics techniques have been used to generate comprehensive lists of protein interactions in a number of species. However, relatively little is known about how these interactions result in functional multiprotein complexes. This gap can be bridged by combining data from proteomics experiments with data from established structure determination techniques. Correspondingly, integrative computational methods are being developed to provide descriptions of protein complexes at varying levels of accuracy and resolution, ranging from complex compositions to detailed atomic structures.
Highlights
ASSEMBLY STRUCTURES OFTEN CANNOT BE RESOLVED BY A SINGLE TECHNIQUEThe structures of macromolecular assemblies in their biologically significant states generally cannot be resolved to atomic resolution by a single technique [14]
The architecture of RNA polymerase II in complex with its initiation factors was determined by combining known crystal structures with data from chemical cross-linking coupled to mass spectrometry [43]
To determine the molecular architecture of the H-RNA POLYMERASE II (RNAPII), we use structural homologs of individual human protein subunits found in the ModBase database [54] (Table II), proteomics data for yeast RNAPII subunits extracted from the BioGRID database [55] (Table III), and an assembly electron density map of H-RNAPII determined at 20-Å resolution by single-particle cryo-Electron microscopy (EM) [50] deposited in the EM data bank [56]
Summary
The structures of macromolecular assemblies in their biologically significant states generally cannot be resolved to atomic resolution by a single technique [14]. In most cases, the resolution of an electron density map is too low to provide a full mechanistic description of a protein complex. Additional techniques, such as high throughput proteomics methods [23], small angle x-ray scattering (SAXS) [24, 25], and fluorescence resonance energy transfer (FRET) spectroscopy [26], are generally limited by low resolution [14] and at times by low accuracy [27,28,29] of the corresponding structural information
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