Specific Protein Domains Research Articles

Neuropeptide Interaction with the Extracellular Domain of the Acid Sensing Ion Channel 1A

Acidic fluctuations occur within the brain and contribute to multiple physiological and patho-physiological processes. Neurons possess specific molecules to sense and respond to these pH changes. In particular, many neurons express the acid sensing ion channels (ASICs). ASICs are ligand-gated ion channels activated by extracellular protons. ASICs are permeable to cations and depolarize neurons to mediate acid-dependent neuronal signaling. Some ASIC channels are also permeable to calcium and these channels are thought to play a particularly important role in neuronal processes. Specifically, ASIC1a subunits form channels permeable to calcium and contribute to multiple behaviors, seizure termination, pain, as well as neuronal death initiated by prolonged acidosis following inflammation and stroke. ASIC1a undergoes a process called steady-state desensitization in which slow, incremental acidification causes the channels to desensitize rather than undergo robust activation. Induction of steady-state desensitization prevents ASIC1a-mediated neuronal death. Yet, specific neuropeptides present within the brain limit steady-state desensitization and allow ASIC1a to activate following slow, incremental acidification. Two types of neuropeptides, the RFamides and dynorphin-related peptides, interact directly with the extracellular domain of ASICs to modulate channel gating. In this work, we explore the mechanism and protein domains responsible for modulation of ASC1a steady-state desensitization by endogenous neuropeptides. We determined that (1) RFamide and dynorphins alter ASIC gating in distinct, but overlapping ways; (2) dynorphins can compete with the inhibitory spider toxin venom peptide PcTx1 for interaction with the channels; and (3) the addition of RFamide and dynorphins synergizes ASIC1a modulation. We also present evidence that specific protein domains are involved in endogenous neuropeptide modulation of ASIC1a. Together, these studies further define endogenous neuropeptides as important modulators of ASIC1a activity and present data indicating that distinct protein domains control neuropeptide effects.

Functional divergence of gene duplicates – a domain-centric view

BackgroundGene duplicates have been shown to evolve at different rates. Here we further investigate the mechanism and functional underpinning of this phenomenon by assessing asymmetric evolution specifically within functional domains of gene duplicates.ResultsBased on duplicate genes in five teleost fishes resulting from a whole genome duplication event, we first show that a Fisher Exact test based approach to detect asymmetry is more sensitive than the previously used Likelihood Ratio test. Using our Fisher Exact test, we found that the evolutionary rate asymmetry in the overall protein is largely explained by the asymmetric evolution within specific protein domains. Moreover, among cases of asymmetrically evolving domains, for the gene copy containing a fast evolving domain, the non-synonymous substitutions often cluster within the fast evolving domain. We found that rare substitutions were preferred within asymmetrically evolving domains suggestive of functional divergence. While overall ~32 % of the domains tested were found to be evolving asymmetrically, certain protein domains such as the Tyrosine and Ser/Thr Kinase domains had a much greater prevalence of asymmetric evolution. Finally, based on the spatial expression of Zebra fish duplicate proteins during development, we found that protein pairs containing asymmetrically evolving domains had a greater divergence in gene expression as compared to the duplicate proteins that did not exhibit asymmetric evolution.ConclusionsTaken together, our results suggest that the previously observed asymmetry in the overall duplicate protein evolution is largely due to divergence of specific domains of the protein, and coincides with divergence in spatial expression domains.

Modular Thermal Sensors in Temperature-Gated TRP Channels

A group of ion channels in the TRP family, the so-called thermal TRP channels, exhibit unprecedentedly strong temperature dependence, some of which reach Q10 > 100 as compared to 2-3 for typical enzymatic reactions. The strong thermal sensitivity of these channels arises because their gating involves large enthalpy changes between closed and open. To quantify the energetics of gating, we applied optically generated submillisecond temperature jumps to directly measure the temperature-dependent activation kinetics. The data show that the opening of TRPV1, for example, is accompanied with an enthalpy change of ∼100 kcal/mol, five times the energetic changes in voltage- or ligand-dependent gating. To gain insights on the energetic source, we analyzed single-channel and macroscopic kinetics of temperature-dependent gating, both showing that temperature has localized effects on specific gating components. Furthermore, the perturbation of membrane compositions, which altered the physical properties of lipids such as temperature-dependent phase transitions, did not abolish temperature activation of the channel. Thus the thermal sensitivity of the channel appears to be intrinsic to the channel itself, most likely arising from a specific protein domain rather than integration of global thermal effects. Using systematic chimeric analysis, we uncovered a proximal N-terminal region to be crucial for temperature sensing in heat-activated TRPVs. Changing this region both successfully transferred thermal sensitivity to temperature-insensitive isoforms and profoundly altered thermal sensing in temperature-sensitive wild-type channels. Swapping other domains including the whole transmembrane core, the C terminus, and the rest of the N terminus had little effect on the large enthalpy of gating. These results support that thermal TRP channels contain modular thermal sensors for their activation by temperature.

An activation domain of plasmid R1 TraI protein delineates stages of gene transfer initiation

Bacterial conjugation is a form of type IV secretion that transports protein and DNA to recipient cells. Specific bacteriophage exploit the conjugative pili and cell envelope spanning protein machinery of these systems to invade bacterial cells. Infection by phage R17 requires F-like pili and coupling protein TraD, which gates the cytoplasmic entrance of the secretion channel. Here we investigate the role of TraD in R17 nucleoprotein uptake and find parallels to secretion mechanisms. The relaxosome of IncFII plasmid R1 is required. A ternary complex of plasmid oriT, TraD and a novel activation domain within the N-terminal 992 residues of TraI contributes a key mechanism involving relaxase-associated properties of TraI, protein interaction and the TraD ATPase. Helicase-associated activities of TraI are dispensable. These findings distinguish for the first time specific protein domains and complexes that process extracellular signals into distinct activation stages in the type IV initiation pathway. The study also provided insights into the evolutionary interplay of phage and the plasmids they exploit. Related plasmid F adapted to R17 independently of TraI. It follows that selection for phage resistance drives not only variation in TraA pilins but diversifies TraD and its binding partners in a plasmid-specific manner.

Deciphering arginine methylation: Tudor tells the tale

Proteins can be modified by post-translational modifications such as phosphorylation, methylation, acetylation and ubiquitylation, creating binding sites for specific protein domains. Methylation has pivotal roles in the formation of complexes that are involved in cellular regulation, including in the generation of small RNAs. Arginine methylation was discovered half a century ago, but the ability of methylarginine sites to serve as binding motifs for members of the Tudor protein family, and the functional significance of the protein-protein interactions that are mediated by Tudor domains, has only recently been appreciated. Tudor proteins are now known to be present in PIWI complexes, where they are thought to interact with methylated PIWI proteins and regulate the PIWI-interacting RNA (piRNA) pathway in the germ line.

ProTeOn and proTeOff, New Protein Devices That Inducibly Activate Bacterial Gene Expression

Using an original workflow, we have modeled, constructed, and characterized two new molecular devices that inducibly activate gene expression in Escherichia coli. The devices, prokaryotic-TetOn and prokaryotic-TetOff, were built by fusing an inducible DNA-binding protein domain to a transcription activation domain and constructing a complementary synthetic promoter sequence through which they could control downstream gene expression. In particular, the transactivators were built using variants of the tetracycline repressor, TetR, and the transactivating domain of the LuxR activator. The complementary promoter sequence included TetR's operator, tetO, and elements of the lux promoter. These specific protein domains and their operator sites were chosen as they have been thoroughly studied and well characterized. First, our methodology began with optimizing the geometry of the molecular components using molecular modeling. We did so to achieve an unprecedented combination of controllable and transactivating function in bacterial organisms. The devices were then built to activate the expression of green fluorescent protein. Their unique function was found to be robustly tight and activating many-fold increases of expressed gene levels, as measured by flow cytometry experiments. The devices were further characterized with stochastic kinetic models. The new devices presented herein may become useful additions to the molecular toolboxes used by biologists to control bacterial gene expression. The methodology used may also be a foundation for the design, development, and characterization of a library of such devices and more complex gene regulatory networks.

Modular thermal sensors in temperature-gated transient receptor potential (TRP) channels

The molecular basis of the thermal sensitivity of temperature-sensitive channels appears to arise from a specific protein domain rather than integration of global thermal effects. Using systematic chimeric analysis, we show that the N-terminal region that connects ankyrin repeats to the first transmembrane segment is crucial for temperature sensing in heat-activated vanilloid receptor channels. Changing this region both transformed temperature-insensitive isoforms into temperature-sensitive channels and significantly perturbed temperature sensing in temperature-sensitive wild-type channels. Swapping other domains such as the transmembrane core, the C terminus, and the rest of the N terminus had little effect on the steepness of temperature dependence. Our results support that thermal transient receptor potential channels contain modular thermal sensors that confer the unprecedentedly strong temperature dependence to these channels.

Modeling the Interactions of the Nucleotide Excision Repair UvrA2 Dimer with DNA

The UvrA protein initiates the DNA damage recognition process by the bacterial nucleotide excision repair (NER) system. Recently, crystallographic structures of holo-UvrA(2) dimers from two different microorganisms have been released (Protein Data Bank entries 2r6f , 2vf7 , and 2vf8 ). However, the details of the DNA binding by UvrA(2) and other peculiarities involved in the damage recognition process remain unknown. We have undertaken a molecular modeling approach to appraise the possible modes of DNA-UvrA(2) interaction using molecular docking and short-scale guided molecular dynamics [continuum field, constrained, and/or unrestricted simulated annealing (SA)], taking into account the three-dimensional location of a series of mutation-identified UvrA residues implicated in DNA binding. The molecular docking was based on the assumptions that the UvrA(2) dimer is preformed prior to DNA binding and that no major protein conformational rearrangements, except moderate domain reorientations, are required for binding of undamaged DNA. As a first approximation, DNA was treated as a rigid ligand. From the electrostatic relief of the ventral surface of UvrA(2), we initially identified three, noncollinear DNA binding paths. Each of the three resulting nucleoprotein complexes (C1, C2, and C3) was analyzed separately, including calculation of binding energies, the number and type of interaction residues (including mutated ones), and the predominant mode of translational and rotational motion of specific protein domains after SA to ensure improved DNA binding. The UvrA(2) dimer can accommodate DNA in all three orientations, albeit with different binding strengths. One of the UvrA(2)-DNA complexes (C1) fulfilled most of the requirements (high interaction energy, proximity of DNA to mutated residues, etc.) expected for a natural, high-affinity DNA binding site. This nucleoprotein presents a structural organization that is designed to clamp and bend double-stranded DNA. We examined the binding site in more detail by docking DNAs of significantly different (AT- vs CG-enriched) sequences and by submitting the complexes to DNA-unrestricted SA. It was found that in a manner independent of the DNA sequence and applied MD protocols, UvrA(2) favors binding of a bent and unwound undamaged DNA, with a kink positioned in the proximity of the Zn3 hairpins, anticollinearly aligned at the bottom of the ventral protein surface. It is further hypothesized that the Zn3 modules play an essential role in the damage recognition process and that the apparent existence of a family of DNA binding sites might be biologically relevant. Our data should prove to be useful in rational (structure-based) mutation studies.

Membrane Topology and DNA-Binding Ability of the Streptococcal CpsA Protein

Many streptococcal pathogens require a polysaccharide capsule for survival in the host during systemic infection. The highly conserved CpsA protein is proposed to be a transcriptional regulator of capsule production in streptococci, although the regulatory mechanism is unknown. Hydropathy plots of CpsA predict an integral membrane protein with 3 transmembrane domains and only 27 cytoplasmic residues, whereas other members of the LytR_cpsA_psr protein family are predicted to have a single transmembrane domain. This unique topology, with the short cytoplasmic domain, membrane localization, and large extracellular domain, suggests a novel mechanism of transcriptional regulation. Therefore, to determine the actual membrane topology of CpsA, specific protein domains were fused to beta-galactosidase or alkaline phosphatase. Enzymatic assays confirmed that the predicted membrane topology for CpsA is correct. To investigate how this integral membrane protein may be functioning in regulation of capsule transcription, purified full-length and truncated forms of CpsA were used in electrophoretic mobility shift assays to characterize the ability to bind the capsule operon promoter. Assays revealed that full-length, purified CpsA protein binds specifically to DNA containing the capsule promoter region. Furthermore, the large extracellular domain is not required for DNA binding, but all cytoplasmic regions of CpsA are necessary and sufficient for specific binding to the capsule operon promoter. This is the first demonstration of a member of this protein family interacting with its target DNA. Taken together, CpsA, as well as other members of the LytR_cpsA_psr protein family, appears to utilize a unique mechanism of transcriptional regulation.

Comparative genomic study of protein disulfide isomerases from photosynthetic organisms

Protein disulfide isomerases (PDIs) are eukaryotic oxidoreductases essential for oxidative protein folding. Their diversity in photosynthetic organisms was assessed by analyzing 24 sequenced genomes belonging to algal, lycophyte, bryophyte and angiosperm phyla. This phylogenetic analysis led to an updated classification into 9 classes (PDI-A to -F, -L, -M and -S) which differed by the number of Trx domains and the presence of additional domains ( D, COPII, J and ARMET). From an evolutionary perspective, the distribution and protein architecture of PDIs differ considerably between algae and terrestrial plants, 5 PDI classes are common whereas 1 is specific to terrestrial plants and 3 to algae. Some algal PDI-Fs possess selenocysteine residues. The PDI family is larger in mammals (19 members in human) than in land plants (around 10 members) and Saccharomyces cerevisiae (5 members). However, PDIs from photosynthetic organisms display an important structural and functional diversity considering their association to specific protein domains.

Knr4 N‐terminal domain controls its localization and function during sexual differentiation and vegetative growth

The Saccharomyces cerevisiae protein Knr4 is composed of a globular central core flanked by two natively disordered regions. Although the central part of the protein holds most of its biological function, the N-terminal domain (amino acids 1-80) is essential in the absence of a functional CWI pathway. We show that this specific protein domain is required for the proper cellular localization of Knr4 at sites of polarized growth during vegetative growth and sexual differentiation (bud tip and 'shmoo' tip). Moreover, Knr4 N-terminal domain is also necessary for cell cycle arrest and shmoo formation in response to pheromone to occur at the correct speed. Thus, the presence of Knr4 at the incipient mating projection site seems important for the establishment of the following polarized growth. Cell wall integrity (CWI) and calcineurin pathways are known to share a common essential function, for which they can substitute for one another. Searching for Knr4 partners responsible for survival in a CWI-defective background, we found that the catalytic subunit of calcineurin Cna1 physically interacts with Knr4 in the yeast two-hybrid assay, in a manner dependent on the presence of the Knr4 N-terminal domain. In addition, we present evidence that Knr4 protein participates in the morphogenesis checkpoint, a safety mechanism that holds the cell cycle in response to bud formation defects or insults in cytoskeleton organization, and in which both the CWI pathway and calcineurin are involved.

Genome-Wide Mapping Indicates That p73 and p63 Co-Occupy Target Sites and Have Similar DNA-Binding Profiles In Vivo

BackgroundThe p53 homologs, p63 and p73, share ∼85% amino acid identity in their DNA-binding domains, but they have distinct biological functions.Principal FindingsUsing chromatin immunoprecipitation and high-resolution tiling arrays covering the human genome, we identify p73 DNA binding sites on a genome-wide level in ME180 human cervical carcinoma cells. Strikingly, the p73 binding profile is indistinguishable from the previously described binding profile for p63 in the same cells. Moreover, the p73∶p63 binding ratio is similar at all genomic loci tested, suggesting that there are few, if any, targets that are specific for one of these factors. As assayed by sequential chromatin immunoprecipitation, p63 and p73 co-occupy DNA target sites in vivo, suggesting that p63 and p73 bind primarily as heterotetrameric complexes in ME180 cells.ConclusionsThe observation that p63 and p73 associate with the same genomic targets suggest that their distinct biological functions are due to cell-type specific expression and/or protein domains that involve functions other than DNA binding.

Differential modulation of mu‐opioid receptor signaling to adenylyl cyclase by regulators of G protein signaling proteins 4 or 8 and 7 in permeabilised C6 cells is Gα subtype dependent

Regulators of G protein signaling (RGS) proteins act as GTPase-accelerating protein to negatively modulate G protein signaling and are defined by a conserved RGS domain with considerable amino acid diversity. To determine the effects of specific, purified RGS proteins on mu-opioid signaling, C6 cells stably expressing a mu-opioid receptor were rendered permeable to proteins by treatment with digitonin. Mu-opioid inhibition of forskolin-stimulated adenylyl cyclase by [D-Ala(2),N-Me-Phe(4),Gly-ol]-enkephalin (DAMGO), a mu-specific opioid peptide, remained fully intact in permeabilized cells. Purified RGS domain of RGS4 added to permeabilized cells resulted in a twofold loss in DAMGO potency but had no effect in cells expressing RGS-insensitive G proteins. The inhibitory effect of DAMGO was reduced to the same extent by purified RGS4 and RGS8. In contrast, the RGS domain of RGS7 had no effect and inhibited the action of RGS8 as a result of weak physical association with Galphai2 and minimal GTPase-accelerating protein activity in C6 cell membranes. These data suggest that differences in conserved RGS domains of specific RGS proteins contribute to differential regulation of opioid signaling to adenylyl cyclase and that a permeabilized cell model is useful for studying the effects of specific RGS proteins on aspects of G protein-coupled receptor signaling.

Protein domains, catalytic activity, and subcellular distribution of mouse NTE-related esterase

A mammalian family of lipid hydrolases, designated "patatin-like phospholipase domain containing (PNPLA)" recently has attracted attention. NTE-related esterase (NRE) as a member of PNPLA is an insulin-regulated lysophospholipase with homology to neuropathy target esterase (NTE). Mouse NRE (mNRE) has a predicted amino-terminal transmembrane region (TM), a putative regulatory (R) domain, and a hydrophobic catalytic (C) domain. In the current study, we described the expression of green fluorescent protein (GFP)-tagged constructs of mNRE and mutant proteins lacking the specific protein domains. Esterase assays indicated that neither the TM nor R-domain was essential for mNRE esterase activity, but the TM significantly contributed to its activity. Subcellular distribution showed that mNRE was anchored in ER via its TM domain and that its C-domain was associated with ER. Furthermore, experiments involving proteinase treatment revealed that most of mNRE molecule was exposed on the cytoplasmic face of ER membranes. Collectively, our results for the first time revealed the protein domains, catalytic activity, and subcellular location of mNRE and a simplified model for mNRE was proposed.

DNA Interaction Kinetics of HIV-1 Nucleocapsid and Gag Proteins

The human immunodeficiency virus type 1 (HIV-1) Gag protein is essential for retroviral assembly. During viral maturation, Gag is processed to form matrix, capsid, and nucleocapsid (NC). NC is initially cleaved into the larger NCp15, then to NCp9, and finally to NCp7. NCp7 functions as a nucleic acid chaperone during retroviral replication, in which it rearranges nucleic acids to facilitate reverse transcription and recombination. The role of Gag and intermediate forms of NC in facilitating nucleic acid remodeling is not well understood, although it is likely that they also function as chaperones during viral assembly and early steps of reverse transcription. To investigate the capability of Gag and precursor forms of NC to act as nucleic acid chaperones, we use single DNA molecule stretching to probe how these proteins alter DNA aggregation, duplex destabilization, and DNA interaction kinetics. These characteristics are critical for efficient nucleic acid chaperone activity. Duplex annealing in the presence of NCp7 indicates that this protein dissociates rapidly from single-stranded DNA. In contrast, Gag inhibits DNA annealing, as indicated by strong hysteresis observed when stretching and relaxing DNA in the presence of Gag. We use a new method to measure the rate at which DNA that has been melted by force is able to reanneal in the presence of Gag and NC proteins. The results show that DNA annealing in the presence of Gag occurs on the time scale of minutes, compared to ∼1 second for annealing in the presence of NCp7. Further studies of reannealing kinetics in the presence of NCp9, NCp15, and Gag deletion constructs will elucidate the role of specific protein domains in determining Gag- and NC-DNA interaction kinetics.

The expanding roles of ITAM adapters FcRγ and DAP12 in myeloid cells

The adapter proteins DAP12 and FcRgamma associate with a wide spectrum of receptors in a variety of innate immune cells to mediate intracellular signaling pathways when their cognate receptor is engaged. These adapter proteins are coupled to their receptors through charged residues within the transmembrane regions of the adapter and receptor. DAP12 and FcRgamma contain specific protein domains (referred to as immunoreceptor tyrosine-based activation motifs) that serve as the substrates and docking sites for kinases, allowing amplification of intracellular signaling reactions. Recent research has broadened the repertoire of receptors that utilize these adapters for signaling to include not only novel immunoglobulin superfamily members but also cytokine receptors, integrins, and other adhesion molecules. There is abundant evidence that these multifunctional signaling adapters also mediate inhibitory activity, downmodulating signaling from Toll-like receptors and other heterologous receptors. In this review, we discuss the newly described receptors that utilize DAP12 and/or FcRgamma adapters to modulate innate immune responses.

The Role of MITF Phosphorylation Sites During Coat Color and Eye Development in Mice Analyzed by Bacterial Artificial Chromosome Transgene Rescue

The microphthalmia-associated transcription factor (Mitf) has emerged as an important model for gene regulation in eukaryotic organisms. In vertebrates, it regulates the development of several cell types including melanocytes and has also been shown to play an important role in melanoma. In vitro, the activity of MITF is regulated by multiple signaling pathways, including the KITL/KIT/B-Raf pathway, which results in phosphorylation of MITF on serine residues 73 and 409. However, the precise role of signaling to MITF in vivo remains largely unknown. Here, we use a BAC transgene rescue approach to introduce specific mutations in MITF to study the importance of specific phospho-acceptor sites and protein domains. We show that mice that carry a BAC transgene where single-amino-acid substitutions have been made in the Mitf gene rescue the phenotype of the loss-of-function mutations in Mitf. This may indicate that signaling from KIT to MITF affects other phospho-acceptor sites in MITF or that alternative sites can be phosphorylated when Ser73 and Ser409 have been mutated. Our results have implications for understanding signaling to transcription factors. Furthermore, as MITF and signaling mechanisms have been shown to play an important role in melanomas, our findings may lead to novel insights into this resilient disease.

Evolutionary Dynamics ofompA, the Gene Encoding theChlamydia trachomatisKey Antigen

Chlamydia trachomatis is the trachoma agent and causes most bacterial sexually transmitted infections worldwide. Its major outer membrane protein (MOMP) is a well-known porin and adhesin and is the dominant antigen. So far, investigation of MOMP variability has been focused mainly on molecular epidemiological surveys. In contrast, we aimed to evaluate the impact of the host pressure on this key antigen by analyzing its evolutionary dynamics in 795 isolates from urogenital infections, taking into account the MOMP secondary structure and the sizes/positions of antigenic regions. One-third of the specimens showed a mutational drift from the corresponding genotype, where approximately 42% of the mutations had never been described. Amino acid alterations were sixfold more frequent within B-cell epitopes than in the remaining protein (P = 0.027), and some mutations were also found within or close to T-cell antigenic clusters. Interestingly, the two most ecologically successful genotypes, E and F, showed a mutation rate 60.3-fold lower than that of the other genotypes (P < 10(-8)), suggesting that their efficacy may be the result of a better fitness in dealing with the host immune system rather than of specific virulence factors. Furthermore, the variability exhibited by some genetic variants involved residues that are known to play a critical role during the membrane mechanical movements, contributing to a more stable and flexible porin conformation, which suggests some plasticity to deal with environmental pressure. Globally, these MOMP mutational trends yielded no mosaic structures or important phylogenetic changes, but instead yielded point mutations on specific protein domains, which may enhance pathogen's infectivity, persistence, and transmission.

Evolution of complexity in the integrin adhesome

Integrin-mediated adhesion is as ancient as multicellularity, but it was not always as complex as it is in humans. Here, I examine the extent of conservation of 192 adhesome proteins across the genomes of nine model organisms spanning one and a half billion years of evolution. The work reveals that Rho GTPases, lipid- and serine/threonine-kinases, and phosphatases existed before integrins, but tyrosine phosphorylation developed concomitant with integrins. The expansion of specific functional groups such as GAPs, GEFs, adaptors, and receptors is demonstrated, along with the expansion of specific protein domains, such as SH3, PH, SH2, CH, and LIM. Expansion is due to gene duplication and creation of families of paralogues. Apparently, these paralogues share few partners and create new sets of interactions, thus increasing specificity and the repertoire of integrin-mediated signaling. Interestingly, the average number of interactions positively correlates with the evolutionary age of proteins. While shedding light on the evolution of adhesome complexity, this analysis also highlights the relevance and creates a framework for studying integrin-mediated adhesion in simpler model organisms.

Navigating the Deubiquitinating Proteome with a CompPASS

Deubiquitinating enzymes (DUBs) act on ubiquitinated substrates to regulate their modification and stability. In this issue, Sowa et al. (2009) present a comprehensive proteomic analysis of DUB interacting proteins in humans and a new quantitative scoring system for hits (CompPASS), providing a resource that links DUBs to biological pathways.