Identification of Human Protein Interaction Domains using an ORFeome-based Yeast Two-hybrid Fragment Library

Physical interactions between proteins are essential for biological processes. Hence, there have been major efforts to elucidate the complete networks of protein–protein interactions, or “interactomes”, of various organisms. Detailed descriptions of protein interaction networks should include information on the discrete domains that mediate these interactions, yet most large-scale efforts model interactions between whole proteins only. We previously developed a yeast two-hybrid-based strategy to systematically map interaction domains and generated a domain-based interactome network for 750 proteins involved in <i>C. elegans</i> early embryonic development. Here, we expand the concept of Y2H-based interaction domain mapping to the genome-wide level. We generated a human fragment library by randomly fragmenting the full-length open reading frames (ORFs) present in the human ORFeome collection. Screens using several proteins required for cell division or polarity establishment as baits demonstrate the ability to accurately identify interaction domains for human proteins using this approach, while the experimental quality of the Y2H data was independently verified in coaffinity purification assays. The library generation strategy can easily be adapted to generate libraries from full-length ORF collections of other organisms

Identification of Human Protein Interaction Domains using an ORFeome-based Yeast Two-hybrid Fragment Library

Physical interactions between proteins are essential for biological processes. Hence, there have been major efforts to elucidate the complete networks of protein–protein interactions, or “interactomes”, of various organisms. Detailed descriptions of protein interaction networks should include information on the discrete domains that mediate these interactions, yet most large-scale efforts model interactions between whole proteins only. We previously developed a yeast two-hybrid-based strategy to systematically map interaction domains and generated a domain-based interactome network for 750 proteins involved in <i>C. elegans</i> early embryonic development. Here, we expand the concept of Y2H-based interaction domain mapping to the genome-wide level. We generated a human fragment library by randomly fragmenting the full-length open reading frames (ORFs) present in the human ORFeome collection. Screens using several proteins required for cell division or polarity establishment as baits demonstrate the ability to accurately identify interaction domains for human proteins using this approach, while the experimental quality of the Y2H data was independently verified in coaffinity purification assays. The library generation strategy can easily be adapted to generate libraries from full-length ORF collections of other organisms

Influence of size and polarity of residue 31 in porcine pancreatic phospholipase A2 on catalytic properties

Residue 31 of porcine pancreatic phospholipase A2 (PLA2) is located at the entrance to the active site. To study the role of residue 31 in PLA2, six mutant enzymes were produced by site-directed mutagenesis, replacing Leu by either Trp, Arg, Ala, Thr, Ser or Gly. Direct binding studies indicated a three to six times greater affinity of the Trp31 PLA2 for both monomeric and micellar substrate analogs, relative to the wild-type enzyme. The other five mutants possess an unchanged affinity for monomers of the product analog n-decylphosphocholine and for micelles of the diacyl substrate analog rac-1,2-dioctanoylamino-dideoxy-glycero-3-phosphocholine. The affinities for micelles of the monoacyl product analog n-hexadecylphosphocholine were decreased 9-20 times for these five mutants. Kinetic studies with monomeric substrates showed that the mutants have Vmax values which range between 15 and 70% relative to the wild-type enzyme. The Vmax values for micelles of the zwitterionic substrate 1,2-dioctanoyl-sn-glycero-3-phosphocholine were lowered 3-50 times. The Km values for the monomeric substrate and the Km values for the micellar substrate were hardly affected in the case of five of the six mutants, but were considerably decreased when Trp was present at position 31. The results of these investigations point to a versatile role for the residue at position 31: involvement in the binding and orientating of monomeric substrate (analogs), involvement in the binding of the enzyme to micellar substrate analogs and possibly involvement in shielding the active site from excess water.

Each of the four intracellular cysteines of CD36 is essential for insulin- or AMP-activated protein kinase-induced CD36 translocation

Stimulation of cellular fatty acid uptake by induction of insulin signalling or AMP-kinase (AMPK) activation is due to translocation of the fatty acid-transporter CD36 from intracellular stores to the plasma membrane (PM). For investigating the role of the four Cys-residues within CD36's cytoplasmic tails in CD36 translocation, we constructed CHO-cells expressing CD36 mutants in which all four, two, or one of the intracellular Cys were replaced by Ser. Intracellular and PM localization of all mutants was similar to wild-type CD36 (CD36wt). Hence, the four Cys do not regulate sub-cellular CD36 localization. However, in contrast to CD36wt, insulin or AMPK activation failed to induce translocation of any of the mutants, indicating that all four intracellular Cys residues are essential for CD36 translocation. The mechanism of defective translocation of mutant CD36 is unknown, but appears not due to loss of S-palmitoylation of the cytoplasmic tails or to aberrant oligomerization of the mutants

A Fullerian Challenge to Legal Intentionalism?

ATAD-3FL and ATADΔETAV are expressed at similar levels. Western blot analysis showing expression levels of ATAD-3 in ATAD-3FL and ATADΔETAV transgenic animals at three different temperatures. (PDF 244 kb

Additional file 4: Table S1. of A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large

All proteins identified, organized by tissue examined. (XLSX 118 kb

Additional file 8: Figure S5. of A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large

a Phylogenetic tree of MAP1-related proteins. Proteins were identified through iterative HMMER searches as implemented in JackHMMER. Three major groups containing the human MAP1A, MAP1B, and MAP1S proteins are color coded. b Sequence alignment of MAPH-1.1 with human MAP1A. (PDF 231 kb

Additional file 6: Table S3. of A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large

Expanded copy of Table 2 in the main text including peptide numbers. (XLSX 14 kb

Additional file 3: Figure S3. of A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large

DNA sequence of the N-terminal GTA tag. Relevant regions are highlighted in color. (PDF 88 kb