Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.

One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a “systems-wide” functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.

Proteasomes are responsible for most intracellular protein degradation in eukaryotes. The 20S proteasome comprises a dyad-symmetric stack of four heptameric rings made from 14 distinct subunits. How it assembles is not understood. Most subunits in the central pair of b-subunit rings are synthesized in precursor form. Normally, the b5 (Doa3) propeptide is essential for yeast proteasome biogenesis, but overproduction of b7 (Pre4) bypasses this requirement. Bypass depends on a unique b7 extension, which contacts the opposing b ring. The resulting proteasomes appear normal but assemble inefficiently, facilitating identification of assembly intermediates. Assembly occurs stepwise into precursor dimers, and intermediates contain the Ump1 assembly factor and a novel complex, Pba1-Pba2. b7 incorporation occurs late and is closely linked to the association of two half-proteasomes. We propose that dimerization is normally driven by the b5 propeptide, an intramolecular chaperone, but b7 addition overcomes an Ump1-dependent assembly checkpoint and stabilizes the precursor dimer.

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Our data are publicly available as a benchmark for further studies of this nature at http://www.cs.toronto.edu/~jenn/LCMS

An ultrasound-guided popliteal sciatic nerve block through a common paraneural sheath at the site of sciatic nerve bifurcation is a simple, safe, and highly effective block technique. It results in consistently short onset time, while respecting the integrity of the epineurium and intraneural structures.

Physicochemical (i.e., sulfhydryl group, protein, and total solubility) as well as functional properties (i.e., water-holding and fat-absorption capacity, foaming and emulsification capacity, and stability) of commercial buttermilk solids (BMS) were compared to nonfat dried milk, soy protein isolate, and dried egg yolk and egg white powders on an equivalent protein basis. BMS showed limited functional properties in water-holding capacity (0.75 g water/g protein) and fat-absorption capacity (1.2 g of oil/g of protein), and foaming capacity (0.5 ml of foam/ml of solution) and stability. However, emulsifying capacity and stability of BMS was not significantly different from other dried protein powders. Results indicated that 0.9 g of protein (approximately 0.45%, wt/vol, concentration) from BMS was needed to emulsify a maximum oil concentration of 50% in water at temperatures up to 50 degrees C. Denaturation of protein, quantified by free sulfhydryl groups, was a critical factor affecting the functionality of BMS and all other protein powders tested. The milk fat globule membrane present in BMS did not enhance either emulsifying capacity or stability.

Editor’s Perspective What We Already Know about This Topic What This Article Tells Us That Is New Background Thoracic paravertebral block is the preferred regional anesthetic technique for breast cancer surgery, but concerns over its invasiveness and risks have prompted search for alternatives. Pectoralis-II block is a promising analgesic technique and potential alternative to paravertebral block, but evidence of its absolute and relative effectiveness versus systemic analgesia (Control) and paravertebral block, respectively, is conflicting. This meta-analysis evaluates the analgesic effectiveness of Pectoralis-II versus Control and paravertebral block for breast cancer surgery. Methods Databases were searched for breast cancer surgery trials comparing Pectoralis-II with Control or paravertebral block. Postoperative oral morphine consumption and difference in area under curve for pooled rest pain scores more than 24 h were designated as coprimary outcomes. Opioid-related side effects, effects on long-term outcomes, such as chronic pain and opioid dependence, were also examined. Results were pooled using random-effects modeling. Results Fourteen randomized trials (887 patients) were analyzed. Compared with Control, Pectoralis-II provided clinically important reductions in 24-h morphine consumption (at least 30.0 mg), by a weighted mean difference [95% CI] of −30.5 mg [−42.2, −18.8] (P < 0.00001), and in rest pain area under the curve more than 24 h, by −4.7cm · h [−5.1, −4.2] or −1.2cm [−1.3, −1.1] per measurement. Compared with paravertebral block, Pectoralis-II was not statistically worse (not different) for 24-h morphine consumption, and not clinically worse for rest pain area under curve more than 24 h. No differences were observed in opioid-related side effects or any other outcomes. Conclusions We found that Pectoralis-II reduces pain intensity and morphine consumption during the first 24 h postoperatively when compared with systemic analgesia alone; and it also offers analgesic benefits noninferior to those of paravertebral block after breast cancer surgery. Evidence supports incorporating Pectoralis-II into multimodal analgesia and also using it as a paravertebral block alternative in this population.