Dual proteome-scale networks reveal cell-specific remodeling of the human interactome

The Interactome of the VAP Family of Proteins: An Overview

“…The resulting Bioplex (Biophysical Interactions of ORFeome-derived complexes) 1 network consisted of more than 20,000 interactions involving 7668 proteins. The network was further enhanced in Bioplex 2 [ 57 ] and recently in Bioplex 3 [ 58 ]. Mining the Bioplex network to search for the interactome of the VAP family of proteins, especially VAPA and VAPB, resulted in many known interaction partners of VAPA/VAPB in addition to new partners ( Figure 4 A).…”

“…More than 250 proteins are reported to interact with VAPA and/or VAPB ( Figure 4 ) [ 22 , 43 , 57 , 58 , 60 ]. Exploring their interactome within the Bioplex network ( Figure 4 A) [ 43 , 57 , 58 ] shows that they share 50% of interacting proteins, the majority of which have FFAT motifs and are involved in lipid transfer between organelles.…”

“…More than 250 proteins are reported to interact with VAPA and/or VAPB ( Figure 4 ) [ 22 , 43 , 57 , 58 , 60 ]. Exploring their interactome within the Bioplex network ( Figure 4 A) [ 43 , 57 , 58 ] shows that they share 50% of interacting proteins, the majority of which have FFAT motifs and are involved in lipid transfer between organelles. For instance, lipid transfer at ER-trans Golgi contact sites is mediated by interaction of FFAT domains of oxysterol binding proteins (OSBPs)/OSBP related proteins (ORPs) and VAPB [ 65 , 66 , 67 , 68 ].…”

“…The discrepancy could be explained by the different experimental setups used in each study. While in affinity purification methods [ 43 , 57 , 58 ] a careful choice of the lysis buffer is necessary to study stable interactions, proximity-based methods have their merits of enriching complexes that are not stable enough in harsh lysis buffer conditions [ 22 , 60 ]. Proteins found in at least two studies are listed in Table 1 .…”

“… The proteins identified in all the three studies are represented in orange. Proteins overlapping in Huttlin et al [ 43 , 57 , 58 ] and Cabukusta et al [ 22 ] are in blue; in Huttlin et al [ 43 , 57 , 58 ] and James et al [ 60 ] in green; and in Cabukusta et al [ 22 ] and James et al [ 60 ] in magenta. Note that several established interaction partners of VAPB, such as CERT and STARD3, do not appear in any of the overlapping sections.…”