Integrative structure modeling of macromolecular assemblies from proteomics data - PubMed (original) (raw)

Fig. 1.

Structural information about a protein assembly. Standard proteomics, biophysical, and computational methods can collectively determine the copy numbers (stoichiometry) and types (composition) of assembly components and predict or experimentally determine protein-protein connectivities (interactivity among a group of proteins) and protein-protein interactions (direct physical interactions). Many of these techniques are capable of a high degree of throughput, allowing for collection of a high volume of data about components of an assembly in a short period of time. Additional biophysical methods can determine distances between components in an assembly, positions of the components, and their relative orientations. Integration of data from varied methods, including low resolution proteomics data, generally increases the accuracy, precision, coverage, and efficiency of structure determination. Methods listed include the following: mass spectrometry (–126), quantitative immunoblotting (127), genetic interactions (128, 129), bioinformatics predictions of protein-protein interactions (130), affinity purification (13, 39, 71, 72), surface plasmon resonance (SPR) (131), Y2H (–116), protein microarrays (–134), protein-fragment complementation assay (PCA) (135, 136), calorimetry (137, 138), FRET (139), bioluminescence resonance energy transfer (BRET) (140), SAXS (24, 25), electron tomography (ET) (21), EM (19, 20, 22), gold labeling (39, 141, 142), green fluorescent protein (GFP) labeling (143), protein-protein docking (144), cross-linking (36, 43, 145, 146), hydrogen/deuterium (H/D) (147), limited proteolysis (148), footprinting (149), x-ray crystallography (15), and NMR spectroscopy (–18).