Structure prediction for CASP8 with all-atom refinement using Rosetta.

We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggressive sampling and all-atom refinement were carried out for nearly all targets. A combination of alignment methodologies was used to generate starting models from a range of templates, and the models were then subjected to Rosetta all atom refinement.

C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation.

The catalytic engine of RNA interference (RNAi) is the RNA-induced silencing complex (RISC), wherein the endoribonuclease Argonaute and single-stranded small interfering RNA (siRNA) direct target mRNA cleavage. We reconstituted long double-stranded RNA- and duplex siRNA-initiated RISC activities with the use of recombinant Drosophila Dicer-2, R2D2, and Ago2 proteins. We used this core reconstitution system to purify an RNAi regulator that we term C3PO (component 3 promoter of RISC), a complex of Translin and Trax.

A JAK2 interdomain linker relays Epo receptor engagement signals to kinase activation.

JAK2 (Janus kinase 2) is essential for cytokine receptor signaling, and several lines of evidence support a causal role of an activating JAK2 mutation in myeloproliferative disorders. JAK2 activity is autoinhibited by its pseudokinase domain in the basal state, and the inhibition is released by cytokine stimulation; how engagement of the cognate receptor triggers this release is unknown. From a functional screen for gain-of-function JAK2 mutations, we discovered 13 missense mutations, nine in the pseudokinase domain and four in the Src homology 2 (SH2)-pseudokinase domain linker.

Remote homology between Munc13 MUN domain and vesicle tethering complexes.

Most core components of the neurotransmitter release machinery have homologues in other types of intracellular membrane traffic, likely underlying a universal mechanism of intracellular membrane fusion. However, no clear similarity between Munc13s and protein families generally involved in membrane traffic has been reported, despite the essential nature of Munc13s for neurotransmitter release. This crucial function was ascribed to a minimal Munc13 region called the MUN domain, which likely participates in soluble N-ethylmaleimide sensitive factor attachment protein receptor complex (SNARE) assembly and is also found in Ca(2+)-dependent activator protein for secretion.

Phenotypic and genotypic analyses of genetic skin disease through the Online Mendelian Inheritance in Man (OMIM) database.

Despite unprecedented gains in genomic technologies and genotype resolution, there remain tremendous challenges in our ability to capture disease "phenomes." We propose a previously unreported method for deconvolving human disease into elemental features, thereby creating a third space that interacts with both the disease and genotypic spaces. Using cutaneous and noncutaneous clinical findings available through Johns Hopkins University's Online Mendelian Inheritance in Man (OMIM) database, we set out to deconstruct genetic skin disease (GSD) into its various components, to more fully explore the relationship between these features within the complex phenotypic space and to characterize the genotypic space within which these disorders exist.

Fido, a novel AMPylation domain common to fic, doc, and AvrB.

Background: The Vibrio parahaemolyticus type III secreted effector VopS contains a fic domain that covalently modifies Rho GTPase threonine with AMP to inhibit downstream signaling events in host cells. The VopS fic domain includes a conserved sequence motif (HPFx[D/E]GN[G/K]R) that contributes to AMPylation. Fic domains are found in a variety of species, including bacteria, a few archaea, and metazoan eukaryotes.

PROCAIN server for remote protein sequence similarity search.

Unlabelled: Sensitive and accurate detection of distant protein homology is essential for the studies of protein structure, function and evolution. We recently developed PROCAIN, a method that is based on sequence profile comparison and involves the analysis of four signals--similarities of residue content at the profile positions combined with three types of assisting information: sequence motifs, residue conservation and predicted secondary structure. Here we present the PROCAIN web server that allows the user to submit a query sequence or multiple sequence alignment and perform the search in a profile database of choice.

Discrete-continuous duality of protein structure space.

Recently, the nature of protein structure space has been widely discussed in the literature. The traditional discrete view of protein universe as a set of separate folds has been criticized in the light of growing evidence that almost any arrangement of secondary structures is possible and the whole protein space can be traversed through a path of similar structures. Here we argue that the discrete and continuous descriptions are not mutually exclusive, but complementary: the space is largely discrete in evolutionary sense, but continuous geometrically when purely structural similarities are quantified.

COMPASS server for homology detection: improved statistical accuracy, speed and functionality.

COMPASS is a profile-based method for the detection of remote sequence similarity and the prediction of protein structure. Here we describe a recently improved public web server of COMPASS, http://prodata.swmed.

The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain-like thiol protease fold.

A Rho GTPase inactivation domain (RID) has been discovered in the multifunctional, autoprocessing RTX toxin RtxA from Vibrio cholerae. The RID domain causes actin depolymerization and rounding of host cells through inactivation of the small Rho GTPases Rho, Rac, and Cdc42. With only a few toxin proteins containing RID domains in the current sequence database, the structure and molecular mechanisms of this domain are unknown.

ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.

Assessing structural similarity and defining common regions through comparison of protein spatial structures is an important task in functional and evolutionary studies of proteins. There are many servers that compare structures and define sub-structures in common between proteins through superposition and closeness of either coordinates or contacts. However, a natural way to analyze a structure for experts working on structure classification is to look for specific three-dimensional (3D) motifs and patterns instead of finding common features in two proteins.

HorA web server to infer homology between proteins using sequence and structural similarity.

The biological properties of proteins are often gleaned through comparative analysis of evolutionary relatives. Although protein structure similarity search methods detect more distant homologs than purely sequence-based methods, structural resemblance can result from either homology (common ancestry) or analogy (similarity without common ancestry). While many existing web servers detect structural neighbors, they do not explicitly address the question of homology versus analogy.

Structure and mechanism of a eukaryotic FMN adenylyltransferase.

Flavin mononucleotide adenylyltransferase (FMNAT) catalyzes the formation of the essential flavocoenzyme flavin adenine dinucleotide (FAD) and plays an important role in flavocoenzyme homeostasis regulation. By sequence comparison, bacterial and eukaryotic FMNAT enzymes belong to two different protein superfamilies and apparently utilize different sets of active-site residues to accomplish the same chemistry. Here we report the first structural characterization of a eukaryotic FMNAT from the pathogenic yeast Candida glabrata.

PROCAIN: protein profile comparison with assisting information.

Detection of remote sequence homology is essential for the accurate inference of protein structure, function and evolution. The most sensitive detection methods involve the comparison of evolutionary patterns reflected in multiple sequence alignments (MSAs) of protein families. We present PROCAIN, a new method for MSA comparison based on the combination of 'vertical' MSA context (substitution constraints at individual sequence positions) and 'horizontal' context (patterns of residue content at multiple positions).

A database of domain definitions for proteins with complex interdomain geometry.

Protein structural domains are necessary for understanding evolution and protein folding, and may vary widely from functional and sequence based domains. Although, various structural domain databases exist, defining domains for some proteins is non-trivial, and definitions of their domain boundaries are not available. Here, we present a novel database of manually defined structural domains for a representative set of proteins from the SCOP "multi-domain proteins" class.

Structure similarity measure with penalty for close non-equivalent residues.

Motivation: Recent improvement in homology-based structure modeling emphasizes the importance of sensitive evaluation measures that help identify and correct modest distortions in models compared with the target structures. Global Distance Test Total Score (GDT_TS), otherwise a very powerful and effective measure for model evaluation, is still insensitive to and can even reward such distortions, as observed for remote homology modeling in the latest CASP8 (Comparative Assessment of Structure Prediction).

Results: We develop a new measure that balances GDT_TS reward for the closeness of equivalent model and target residues ('attraction' term) with the penalty for the closeness of non-equivalent residues ('repulsion' term).

CPDadh: a new peptidase family homologous to the cysteine protease domain in bacterial MARTX toxins.

A cysteine protease domain (CPD) has been recently discovered in a group of multifunctional, autoprocessing RTX toxins (MARTX) and Clostridium difficile toxins A and B. These CPDs (referred to as CPDmartx) autocleave the toxins to release domains with toxic effects inside host cells. We report identification and computational analysis of CPDadh, a new cysteine peptidase family homologous to CPDmartx.

Prediction of a caspase-like fold in Tannerella forsythia virulence factor PrtH.

Tannerella forsythia is a bacterial pathogen involved in periodontal disease. A cysteine protease PrtH has been characterized in this bacterium as a virulence factor. PrtH has the activity of detaching adherent cells from substratum, and the level of PrtH is associated with periodontal attachment loss.

Genetic variation in ANGPTL4 provides insights into protein processing and function.

Angiopoietin-like protein 4 (ANGPTL4) is a secreted protein that modulates the disposition of circulating triglycerides (TG) by inhibiting lipoprotein lipase (LPL). Here we examine the steps involved in the synthesis and post-translational processing of ANGPTL4, and the effects of a naturally occurring sequence variant (E40K) that is associated with lower plasma TG levels in humans. Expression of the wild-type and mutant proteins in HEK-293A cells indicated that ANGPTL4 formed dimers and tetramers in cells prior to secretion and cleavage of the protein.

The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif.

Background: Argonaute (Ago) proteins interact with small regulatory RNAs to mediate gene regulatory pathways. A recent report by Kiriakidou et al. 1 describes an MC sequence region identified in Ago2 that displays similarity to the cap-binding motif in translation initiation factor 4E (eIF4E).

Genetic defects in surfactant protein A2 are associated with pulmonary fibrosis and lung cancer.

Idiopathic pulmonary fibrosis (IPF) is a lethal scarring lung disease that affects older adults. Heterozygous rare mutations in the genes encoding telomerase are found in approximately 15% of familial cases. We have used linkage to map another disease-causing gene in a large family with IPF and adenocarcinoma of the lung to a 15.

AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling.

The Vibrio parahaemolyticus type III effector VopS is implicated in cell rounding and the collapse of the actin cytoskeleton by inhibiting Rho guanosine triphosphatases (GTPases). We found that VopS could act to covalently modify a conserved threonine residue on Rho, Rac, and Cdc42 with adenosine 5'-monophosphate (AMP). The resulting AMPylation prevented the interaction of Rho GTPases with downstream effectors, thereby inhibiting actin assembly in the infected cell.

Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli.

Lysine acetylation and its regulatory enzymes are known to have pivotal roles in mammalian cellular physiology. However, the extent and function of this modification in prokaryotic cells remain largely unexplored, thereby presenting a hurdle to further functional study of this modification in prokaryotic systems. Here we report the first global screening of lysine acetylation, identifying 138 modification sites in 91 proteins from Escherichia coli.

PROMALS3D web server for accurate multiple protein sequence and structure alignments.

Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods.