Surprising similarities in structure comparison

Prediction of protein functions

The recent explosion in the number and diversity of novel proteins identified by the large-scale "omics" technologies poses new and important questions to the blossoming field of systems biology--what are all these proteins, how did they come about, and most importantly, what do they do? From a comparatively small number of protein structural domains a staggering array of structural variants has evolved, which has in turn facilitated an expanse of functional derivatives. This review considers the primary mechanisms that have contributed to the vastness of our existing, and expanding, protein repertoires, while also outlining the protocols available for elucidating their true biological function. The various function prediction programs available, both sequence and structure based, are discussed and their associated strengths and weaknesses outlined.

Touring protein space with Matt

Using the Matt structure alignment program, we take a tour of protein space, producing a hierarchical clustering scheme that divides protein structural domains into clusters based on geometric dissimilarity. While it was known that purely structural, geometric, distance-based measures of structural similarity, such as Dali/FSSP, could largely replicate hand-curated schemes such as SCOP at the family level, it was an open question as to whether any such scheme could approximate SCOP at the more distant superfamily and fold levels. We partially answer this question in the affirmative, by designing a clustering scheme based on Matt that approximately matches SCOP at the superfamily level, and demonstrates qualitative differences in performance between Matt and DaliLite. Implications for the debate over the organization of protein fold space are discussed. Based on our clustering of protein space, we introduce the Mattbench benchmark set, a new collection of structural alignments useful for testing sequence aligners on more distantly homologous proteins.

PDB-2-PB: a curated online protein block sequence database

This article describes the development of a curated online protein block sequence database, PDB-2-PB. The protein block sequences for protein structures with complete backbone coordinates have been encoded using the encoding procedure of de Brevern, Etchebest & Hazout [Proteins(2000),41, 271–287]. In the current release of the PDB-2-PB database (version 1.0), the protein entries from a recent release of the World Wide Protein Data Bank (wwPDB), which has 74 297 solved PDB entries as of 7 July 2011, have been used as a primary source. The PDB-2-PB database stores the protein block sequences for all the chains present in a protein structure. PDB-2-PB version 1.0 has the curated protein block sequences for 103 252 PDB chain entries (93 547 X-ray, 7033 NMR and 2672 other experimental chain entries). From the PDB-2-PB database, users can extract the curated protein block sequence and its corresponding amino acid sequence, which is extracted from the PDB ATOM records. Users can download these sequences either by using the PDB code or by using various parameters listed in the database. The PDB-2-PB database is freely available at http://bioinfo.bdu.ac.in/~pb/.

Modulating protein-protein interactions with small molecules: the importance of binding hotspots

The modulation of protein-protein interactions (PPIs) by small drug-like molecules is a relatively new area of research and has opened up new opportunities in drug discovery. However, the progress made in this area is limited to a handful of known cases of small molecules that target specific diseases. With the increasing availability of protein structure complexes, it is highly important to devise strategies exploiting homologous structure space on a large scale for discovering putative PPIs that could be attractive drug targets. Here, we propose a scheme that allows performing large-scale screening of all protein complexes and finding putative small-molecule and/or peptide binding sites overlapping with protein-protein binding sites (so-called "multibinding sites"). We find more than 600 nonredundant proteins from 60 protein families with multibinding sites. Moreover, we show that the multibinding sites are mostly observed in transient complexes, largely overlap with the binding hotspots and are more evolutionarily conserved than other interface sites. We investigate possible mechanisms of how small molecules may modulate protein-protein binding and discuss examples of new candidates for drug design.

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

MMDB: 3D structures and macromolecular interactions

Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure.

MatAlign: PRECISE PROTEIN STRUCTURE COMPARISON BY MATRIX ALIGNMENT

We propose a detailed protein structure alignment method named "MatAlign". It is a two-step algorithm. Firstly, we represent 3D protein structures as 2D distance matrices, and align these matrices by means of dynamic programming in order to find the initially aligned residue pairs. Secondly, we refine the initial alignment iteratively into the optimal one according to an objective scoring function. We compare our method against DALI and CE, which are among the most accurate and the most widely used of the existing structural comparison tools. On the benchmark set of 68 protein structure pairs by Fischer et al., MatAlign provides better alignment results, according to four different criteria, than both DALI and CE in a majority of cases. MatAlign also performs as well in structural database search as DALI does, and much better than CE does. MatAlign is about two to three times faster than DALI, and has about the same speed as CE. The software and the supplementary information for this paper are available at . .

PROTEIN STRUCTURE ALIGNMENT AND FAST SIMILARITY SEARCH USING LOCAL SHAPE SIGNATURES

We present a new method for conducting protein structure similarity searches, which improves on the efficiency of some existing techniques. Our method is grounded in the theory of differential geometry on 3D space curve matching. We generate shape signatures for proteins that are invariant, localized, robust, compact, and biologically meaningful. The invariancy of the shape signatures allows us to improve similarity searching efficiency by adopting a hierarchical coarse-to-fine strategy. We index the shape signatures using an efficient hashing-based technique. With the help of this technique we screen out unlikely candidates and perform detailed pairwise alignments only for a small number of candidates that survive the screening process. Contrary to other hashing based techniques, our technique employs domain specific information (not just geometric information) in constructing the hash key, and hence, is more tuned to the domain of biology. Furthermore, the invariancy, localization, and compactness of the shape signatures allow us to utilize a well-known local sequence alignment algorithm for aligning two protein structures. One measure of the efficacy of the proposed technique is that we were able to perform structure alignment queries 36 times faster (on the average) than a well-known method while keeping the quality of the query results at an approximately similar level.

ITERATIVE NON-SEQUENTIAL PROTEIN STRUCTURAL ALIGNMENT

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at

TOWARDS SCALEable PROTEIN STRUCTURE COMPARISON AND DATABASE SEARCH

Comparing protein structures in three dimensions is a computationally expensive process that makes a full scan of a protein against a library of known protein structures impractical. To reduce the cost, we can use an approximation of the three dimensional structure that allows protein comparison to be performed quickly to filter away dissimilar proteins. In this paper, we present a new algorithm, called SCALE, for protein structure comparison. In SCALE, a protein is represented as a sequence of secondary structure elements (SSEs) augmented with 3D structural properties such as the distances and angles between the SSEs. As such, the comparison between two proteins is reduced to a sequence alignment problem between their corresponding sequences of SSEs. The 3-D structural properties of the proteins contribute to the similarity score between the two sequences. We have implemented SCALE, and compared its performance against existing schemes. Our performance study shows that SCALE outperforms existing methods in terms of both efficiency and effectiveness (measured in terms of precision and recall). To avoid exhaustive search, an index based on the structural properties is also proposed. The index prunes away a considerable amount of dissimilar proteins given a query protein.

Divergence and convergence in enzyme evolution

Comparative analysis of the sequences of enzymes encoded in a variety of prokaryotic and eukaryotic genomes reveals convergence and divergence at several levels. Functional convergence can be inferred when structurally distinct and hence non-homologous enzymes show the ability to catalyze the same biochemical reaction. In contrast, as a result of functional diversification, many structurally similar enzyme molecules act on substantially distinct substrates and catalyze diverse biochemical reactions. Here, we present updates on the ATP-grasp, alkaline phosphatase, cupin, HD hydrolase, and N-terminal nucleophile (Ntn) hydrolase enzyme superfamilies and discuss the patterns of sequence and structural conservation and diversity within these superfamilies. Typically, enzymes within a superfamily possess common sequence motifs and key active site residues, as well as (predicted) reaction mechanisms. These observations suggest that the strained conformation (the entatic state) of the active site, which is responsible for the substrate binding and formation of the transition complex, tends to be conserved within enzyme superfamilies. The subsequent fate of the transition complex is not necessarily conserved and depends on the details of the structures of the enzyme and the substrate. This variability of reaction outcomes limits the ability of sequence analysis to predict the exact enzymatic activities of newly sequenced gene products. Nevertheless, sequence-based (super)family assignments and generic functional predictions, even if imprecise, provide valuable leads for experimental studies and remain the best approach to the functional annotation of uncharacterized proteins from new genomes.

From lipid transport to oxygenation of aromatic compounds: evolution within the Bet v1-like superfamily

In absence of significant sequence similarity, remote homology between proteins can be confused with analogy and in such a case, shared ancestry can be inferred in light of certain unique and common features. In the present study, to understand the evolutionary origin of catalytic domain of large subunit of ring-hydroxylating oxygenases (RHOs), belonging to the Bet v1-like superfamily, structure-based phylogenies have been derived from structural alignment of representative proteins of the superfamily. A careful inspection of the structural relatedness of RHOs with the rest of the families showed closest similarity between RHO catalytic domain and PA1206-like protein. In addition, phylogenetic relationship of the Rieske domain of the large subunit of RHOs with functionally and structurally similar proteins has also been elucidated so as to postulate the most possible events leading to the genesis of the large subunit of RHOs.

Structure of the glycosyltransferase EryCIII in complex with its activating P450 homologue EryCII

In the biosynthesis of the clinically important antibiotic erythromycin D, the glycosyltransferase (GT) EryCIII, in concert with its partner EryCII, attaches a nucleotide-activated sugar to the macrolide scaffold with high specificity. To understand the role of EryCII, we have determined the crystal structure of the EryCIII·EryCII complex at 3.1 Å resolution. The structure reveals a heterotetramer with a distinctive, elongated quaternary organization. The EryCIII subunits form an extensive self-complementary dimer interface at the center of the complex, and the EryCII subunits lie on the periphery. EryCII binds in the vicinity of the putative macrolide binding site of EryCIII but does not make direct interactions with this site. Our biophysical and enzymatic data support a model in which EryCII stabilizes EryCIII and also functions as an allosteric activator of the GT.

The Histone Database: an integrated resource for histones and histone fold-containing proteins

Eukaryotic chromatin is composed of DNA and protein components-core histones-that act to compactly pack the DNA into nucleosomes, the fundamental building blocks of chromatin. These nucleosomes are connected to adjacent nucleosomes by linker histones. Nucleosomes are highly dynamic and, through various core histone post-translational modifications and incorporation of diverse histone variants, can serve as epigenetic marks to control processes such as gene expression and recombination. The Histone Sequence Database is a curated collection of sequences and structures of histones and non-histone proteins containing histone folds, assembled from major public databases. Here, we report a substantial increase in the number of sequences and taxonomic coverage for histone and histone fold-containing proteins available in the database. Additionally, the database now contains an expanded dataset that includes archaeal histone sequences. The database also provides comprehensive multiple sequence alignments for each of the four core histones (H2A, H2B, H3 and H4), the linker histones (H1/H5) and the archaeal histones. The database also includes current information on solved histone fold-containing structures. The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins.

CASP9 target classification

The Critical assessment of protein structure prediction round 9 (CASP9) aimed to evaluate predictions for 129 experimentally determined protein structures. To assess tertiary structure predictions, these target structures were divided into domain-based evaluation units that were then classified into two assessment categories: template based modeling (TBM) and template free modeling (FM). CASP9 targets were split into domains of structurally compact evolutionary modules. For the targets with more than one defined domain, the decision to split structures into domains for evaluation was based on server performance. Target domains were categorized based on their evolutionary relatedness to existing templates as well as their difficulty levels indicated by server performance. Those target domains with sequence-related templates and high server prediction performance were classified as TMB, whereas those targets without identifiable templates and low server performance were classified as FM. However, using these generalizations for classification resulted in a blurred boundary between CASP9 assessment categories. Thus, the FM category included those domains without sequence detectable templates (25 target domains) as well as some domains with difficult to detect templates whose predictions were as poor as those without templates (five target domains). Several interesting examples are discussed, including targets with sequence related templates that exhibit unusual structural differences, targets with homologous or analogous structure templates that are not detectable by sequence, and targets with new folds.

Crystal structure of sulfotransferase STF9 from Mycobacterium avium

Sulfotransferases catalyze the sulfate conjugation of a wide variety of endogenous and exogenous molecules. Human pathogenic mycobacteria produce numerous sulfated molecules including sulfolipids which are well related to the virulence of several strains. The genome of Mycobacterium avium encodes eight putative sulfotransferases (stf1, stf4-stf10). Among them, STF9 shows higher similarity to human heparan sulfate 3-O-sulfotransferase isoforms than to the bacterial STs. Here, we determined the crystal structure of sulfotransferase STF9 in complex with a sulfate ion and palmitic acid at a resolution of 2.6 Å. STF9 has a spherical structure utilizing the classical sulfotransferase fold. STF9 exclusively possesses three N-terminal α-helices (α1, α2, α3) parallel to the 3'-phosphoadenosine-5'-phosphosulfate (PAPS) binding motif. The sulfate ion binds to the PAPS binding structural motif and the palmitic acid molecule binds in the deep cleft of the predicted substrate binding site suggesting the nature of endogenous acceptor substrate of STF9 resembles palmitic acid. The substrate binding site is covered by a flexible loop which may have involvement in endogenous substrate recognition. Based on the mutational study (Hossain et al., Mol Cell Biochem 350:155-162; 2011) and structural resemblance of STF9-sulfate ion-palmitic acid complex to the hHS3OST3 complex with PAP (3'-phosphoadenosine-5'-phosphate) and an acceptor sugar chain, Glu170 and Arg96 are appeared to be catalytic residues in STF9 sulfuryl transfer mechanism.

Unusual, dual endo- and exonuclease activity in the degradosome explained by crystal structure analysis of RNase J1

RNase J is an essential enzyme in Bacillus subtilis with unusual dual endonuclease and 5'-to-3' exonuclease activities that play an important role in the maturation and degradation of mRNA. RNase J is also a component of the recently identified "degradosome" of B. subtilis. We report the crystal structure of RNase J1 from B. subtilis to 3.0 Å resolution, analysis of which reveals it to be in an open conformation suitable for binding substrate RNA. RNase J is a member of the β-CASP family of zinc-dependent metallo-β-lactamases. We have exploited this similarity in constructing a model for an RNase J1:RNA complex. Analysis of this model reveals candidate-stacking interactions with conserved aromatic side chains, providing a molecular basis for the observed enzyme activity. Comparisons of the B. subtilis RNase J structure with related enzymes reveal key differences that provide insights into conformational changes during catalysis and the role of the C-terminal domain.

Critical assessment of structure-based sequence alignment methods at distant relationships

Accurate sequence alignments are crucial for modelling and to provide an evolutionary picture of related proteins. It is well-known that alignments are hard to obtain during distant relationships. Three thousand and fifty-two alignments of 218 pairs of protein domain structural entries, with <40% sequence identity, belonging to different structural classes, of diverse domain sizes and length-rigid/variable domains were performed using 12 programs. Structural parameters such as root mean square deviation, secondary-structural content and equivalences were considered for critical assessment. Methods that compare fragments and permit twists and translations align well during distant relationships and length variations.

Characterization of the deoxynucleotide triphosphate triphosphohydrolase (dNTPase) activity of the EF1143 protein from Enterococcus faecalis and crystal structure of the activator-substrate complex

The EF1143 protein from Enterococcus faecalis is a distant homolog of deoxynucleotide triphosphate triphosphohydrolases (dNTPases) from Escherichia coli and Thermus thermophilus. These dNTPases are important components in the regulation of the dNTP pool in bacteria. Biochemical assays of the EF1143 dNTPase activity demonstrated nonspecific hydrolysis of all canonical dNTPs in the presence of Mn(2+). In contrast, with Mg(2+) hydrolysis required the presence of dGTP as an effector, activating the degradation of dATP and dCTP with dGTP also being consumed in the reaction with dATP. The crystal structure of EF1143 and dynamic light scattering measurements in solution revealed a tetrameric oligomer as the most probable biologically active unit. The tetramer contains four dGTP specific allosteric regulatory sites and four active sites. Examination of the active site with the dATP substrate suggests an in-line nucleophilic attack on the α-phosphate center as a possible mechanism of the hydrolysis and two highly conserved residues, His-129 and Glu-122, as an acid-base catalytic dyad. Structural differences between EF1143 apo and holo forms revealed mobility of the α3 helix that can regulate the size of the active site binding pocket and could be stabilized in the open conformation upon formation of the tetramer and dGTP effector binding.

Crenarchaeal CdvA forms double-helical filaments containing DNA and interacts with ESCRT-III-like CdvB

BACKGROUND

The phylum Crenarchaeota lacks the FtsZ cell division hallmark of bacteria and employs instead Cdv proteins. While CdvB and CdvC are homologues of the eukaryotic ESCRT-III and Vps4 proteins, implicated in membrane fission processes during multivesicular body biogenesis, cytokinesis and budding of some enveloped viruses, little is known about the structure and function of CdvA. Here, we report the biochemical and biophysical characterization of the three Cdv proteins from the hyperthermophilic archaeon Metallospherae sedula.

METHODOLOGY/PRINCIPAL FINDINGS

Using sucrose density gradient ultracentrifugation and negative staining electron microscopy, we evidenced for the first time that CdvA forms polymers in association with DNA, similar to known bacterial DNA partitioning proteins. We also observed that, in contrast to full-lengh CdvB that was purified as a monodisperse protein, the C-terminally deleted CdvB construct forms filamentous polymers, a phenomenon previously observed with eukaryotic ESCRT-III proteins. Based on size exclusion chromatography data combined with detection by multi-angle laser light scattering analysis, we demonstrated that CdvC assembles, in a nucleotide-independent way, as homopolymers resembling dodecamers and endowed with ATPase activity in vitro. The interactions between these putative cell division partners were further explored. Thus, besides confirming the previous observations that CdvB interacts with both CdvA and CdvC, our data demonstrate that CdvA/CdvB and CdvC/CdvB interactions are not mutually exclusive.

CONCLUSIONS/SIGNIFICANCE

Our data reinforce the concept that Cdv proteins are closely related to the eukaryotic ESCRT-III counterparts and suggest that the organization of the ESCRT-III machinery at the Crenarchaeal cell division septum is organized by CdvA an ancient cytoskeleton protein that might help to coordinate genome segregation.

Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE)

In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.

Searching NCBI databases using Entrez

One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two basic protocols describe simple, text-based searches, illustrating the types of information that can be retrieved through the Entrez system. An alternate protocol builds upon the first basic protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query. The support protocol reviews how to save frequently issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.

Crystal structure of the novel PaiA N-acetyltransferase from Thermoplasma acidophilum involved in the negative control of sporulation and degradative enzyme production

GCN5-related N-acetyltransferases (GNATs) are the most widely distributed acetyltransferase systems among all three domains of life. GNATs appear to be involved in several key processes, including microbial antibiotic resistance, compacting eukaryotic DNA, controlling gene expression, and protein synthesis. Here, we report the crystal structure of a putative GNAT Ta0374 from Thermoplasma acidophilum, a hyperacidophilic bacterium, that has been determined in an apo-form, in complex with its natural ligand (acetyl coenzyme A), and in complex with a product of reaction (coenzyme A) obtained by cocrystallization with spermidine. Sequence and structural analysis reveals that Ta0374 belongs to a novel protein family, PaiA, involved in the negative control of sporulation and degradative enzyme production. The crystal structure of Ta0374 confirms that it binds acetyl coenzyme A in a way similar to other GNATs and is capable of acetylating spermidine. Based on structural and docking analysis, it is expected that Glu53 and Tyr93 are key residues for recognizing spermidine. Additionally, we find that the purification His-Tag in the apo-form structure of Ta0374 prevents binding of acetyl coenzyme A in the crystal, though not in solution, and affects a chain-flip rotation of "motif A" which is the most conserved sequence among canonical acetyltransferases.

Crystal structure of a putative transcriptional regulator SCO0520 from Streptomyces coelicolor A3(2) reveals an unusual dimer among TetR family proteins

A structure of the apo-form of the putative transcriptional regulator SCO0520 from Streptomyces coelicolor A3(2) was determined at 1.8 Å resolution. SCO0520 belongs to the TetR family of regulators. In the crystal lattice, the asymmetric unit contains two monomers that form an Ω-shaped dimer. The distance between the two DNA-recognition domains is much longer than the corresponding distances in the known structures of other TetR family proteins. In addition, the subunits in the dimer have different conformational states, resulting in different relative positions of the DNA-binding and regulatory domains. Similar conformational modifications are observed in other TetR regulators and result from ligand binding. These studies provide information about the flexibility of SCO0520 molecule and its putative biological function.

iPBA: a tool for protein structure comparison using sequence alignment strategies

With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman–Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of ∼88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA⁺ in >80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient ‘sequence-based’ structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/.

Optimization of a cyclic peptide inhibitor of Ser/Thr phosphatase PPM1D (Wip1)

PPM1D (PP2Cδ or Wip1) was identified as a wild-type p53-induced Ser/Thr phosphatase that accumulates after DNA damage and classified into the PP2C family. It dephosphorylates and inactivates several proteins critical for cellular stress responses, including p38 MAPK, p53, and ATM. Furthermore, PPM1D is amplified and/or overexpressed in a number of human cancers. Thus, inhibition of its activity could constitute an important new strategy for therapeutic intervention to halt the progression of several different cancers. Previously, we reported the development of a cyclic thioether peptide with low micromolar inhibitory activity toward PPM1D. Here, we describe important improvements in the inhibitory activity of this class of cyclic peptides and also present a binding model based upon the results. We found that specific interaction of an aromatic ring at the X1 position and negative charge at the X5 and X6 positions significantly increased the inhibitory activity of the cyclic peptide, with the optimized molecule having a K(i) of 110 nM. To the best of our knowledge, this represents the highest inhibitory activity reported for an inhibitor of PPM1D. We further developed an inhibitor selective for PPM1D over PPM1A with a K(i) of 2.9 μM. Optimization of the cyclic peptide and mutagenesis experiments suggest that a highly basic loop unique to PPM1D is related to substrate specificity. We propose a new model for the catalytic site of PPM1D and inhibition by the cyclic peptides that will be useful both for the subsequent design of PPM1D inhibitors and for identification of new substrates.

Improvement of protein structure comparison using a structural alphabet

The three dimensional structure of a protein provides major insights into its function. Protein structure comparison has implications in functional and evolutionary studies. A structural alphabet (SA) is a library of local protein structure prototypes that can abstract every part of protein main chain conformation. Protein Blocks (PBs) is a widely used SA, composed of 16 prototypes, each representing a pentapeptide backbone conformation defined in terms of dihedral angles. Through this description, the 3D structural information can be translated into a 1D sequence of PBs. In a previous study, we have used this approach to compare protein structures encoded in terms of PBs. A classical sequence alignment procedure based on dynamic programming was used, with a dedicated PB Substitution Matrix (SM). PB-based pairwise structural alignment method gave an excellent performance, when compared to other established methods for mining. In this study, we have (i) refined the SMs and (ii) improved the Protein Block Alignment methodology (named as iPBA). The SM was normalized in regards to sequence and structural similarity. Alignment of protein structures often involves similar structural regions separated by dissimilar stretches. A dynamic programming algorithm that weighs these local similar stretches has been designed. Amino acid substitutions scores were also coupled linearly with the PB substitutions. iPBA improves (i) the mining efficiency rate by 6.8% and (ii) more than 82% of the alignments have a better quality. A higher efficiency in aligning multi-domain proteins could be also demonstrated. The quality of alignment is better than DALI and MUSTANG in 81.3% of the cases. Thus our study has resulted in an impressive improvement in the quality of protein structural alignment.

Maximum contact map overlap revisited

Among the measures for quantifying the similarity between three-dimensional (3D) protein structures, maximum contact map overlap (CMO) received sustained attention during the past decade. Despite this, the known algorithms exhibit modest performance and are not applicable for large-scale comparison. This article offers a clear advance in this respect. We present a new integer programming model for CMO and propose an exact branch-and-bound algorithm with bounds obtained by a novel Lagrangian relaxation. The efficiency of the approach is demonstrated on a popular small benchmark (Skolnick set, 40 domains). On this set, our algorithm significantly outperforms the best existing exact algorithms. Many hard CMO instances have been solved for the first time. To further assess our approach, we constructed a large-scale set of 300 protein domains. Computing the similarity measure for any of the 44850 pairs, we obtained a classification in excellent agreement with SCOP. Supplementary Material is available at www.liebertonline.com/cmb.

The conserved Candida albicans CA3427 gene product defines a new family of proteins exhibiting the generic periplasmic binding protein structural fold

Nosocomial diseases due to Candida albicans infections are in constant rise in hospitals, where they cause serious complications to already fragile intensive care patients. Antifungal drug resistance is fast becoming a serious issue due to the emergence of strains resistant to currently available antifungal agents. Thus the urgency to identify new potential protein targets, the function and structure of which may guide the development of new antifungal drugs. In this context, we initiated a comparative genomics study in search of promising protein coding genes among the most conserved ones in reference fungal genomes. The CA3427 gene was selected on the basis of its presence among pathogenic fungi contrasting with its absence in the non pathogenic Saccharomyces cerevisiae. We report the crystal 3D-structure of the Candida albicans CA3427 protein at 2.1 Å resolution. The combined analysis of its sequence and structure reveals a structural fold originally associated with periplasmic binding proteins. The CA3427 structure highlights a binding site located between the two protein domains, corresponding to a sequence segment conserved among fungi. Two crystal forms of CA3427 were found, suggesting that the presence or absence of a ligand at the proposed binding site might trigger a “Venus flytrap” motion, coupled to the previously described activity of bacterial periplasmic binding proteins. The conserved binding site defines a new subfamily of periplasmic binding proteins also found in many bacteria of the bacteroidetes division, in a choanoflagellate (a free-living unicellular and colonial flagellate eukaryote) and in a placozoan (the closest multicellular relative of animals). A phylogenetic analysis suggests that this gene family originated in bacteria before its horizontal transfer to an ancestral eukaryote prior to the radiation of fungi. It was then lost by the Saccharomycetales which include Saccharomyces cerevisiae.

Protein-protein binding site prediction by local structural alignment

Generalization of an earlier algorithm has led to the development of new local structural alignment algorithms for prediction of protein-protein binding sites. The algorithms use maximum cliques on protein graphs to define structurally similar protein regions. The search for structural neighbors in the new algorithms has been extended to all the proteins in the PDB and the query protein is compared to more than 60,000 proteins or over 300,000 single-chain structures. The resulting structural similarities are combined and used to predict the protein binding sites. This study shows that the location of protein binding sites can be predicted by comparing only local structural similarities irrespective of general protein folds.

A mathematical framework for protein structure comparison

Comparison of protein structures is important for revealing the evolutionary relationship among proteins, predicting protein functions and predicting protein structures. Many methods have been developed in the past to align two or multiple protein structures. Despite the importance of this problem, rigorous mathematical or statistical frameworks have seldom been pursued for general protein structure comparison. One notable issue in this field is that with many different distances used to measure the similarity between protein structures, none of them are proper distances when protein structures of different sequences are compared. Statistical approaches based on those non-proper distances or similarity scores as random variables are thus not mathematically rigorous. In this work, we develop a mathematical framework for protein structure comparison by treating protein structures as three-dimensional curves. Using an elastic Riemannian metric on spaces of curves, geodesic distance, a proper distance on spaces of curves, can be computed for any two protein structures. In this framework, protein structures can be treated as random variables on the shape manifold, and means and covariance can be computed for populations of protein structures. Furthermore, these moments can be used to build Gaussian-type probability distributions of protein structures for use in hypothesis testing. The covariance of a population of protein structures can reveal the population-specific variations and be helpful in improving structure classification. With curves representing protein structures, the matching is performed using elastic shape analysis of curves, which can effectively model conformational changes and insertions/deletions. We show that our method performs comparably with commonly used methods in protein structure classification on a large manually annotated data set.

Protein structure comparison is important for understanding the evolutionary relationships among proteins, predicting protein functions, and predicting protein structures. Despite its importance, there have been no rigorous mathematical or statistical frameworks for protein structure comparison. One notable issue in this field is that with many different similarity measures used in comparing protein structures, none of them are proper distances when protein structures of different sequences are compared. In this study, we develop a mathematical framework for protein structure comparison by treating protein structures as three dimensional curves. A formal distance, geodesic distance, can be computed for any two protein structures. In this framework, population-specific variations within protein families can be characterized through building probability distributions for structures of protein families. The mean and covariance computed from groups of protein structures can also help to improve the classifications of protein structures. With curves representing protein structures, the matching is performed using elastic shape analysis of curves, which can effectively model conformational changes and insertions/deletions.

Switching from an esterase to a hydroxynitrile lyase mechanism requires only two amino acid substitutions

The alpha/beta hydrolase superfamily contains mainly esterases, which catalyze hydrolysis, but also includes hydroxynitrile lyases, which catalyze addition of cyanide to aldehydes, a carbon-carbon bond formation. Here, we convert a plant esterase, SABP2, into a hydroxynitrile lyase using just two amino acid substitutions. Variant SABP2-G12T-M239K lost the ability to catalyze ester hydrolysis (<0.9 mU/mg) and gained the ability to catalyze the release of cyanide from mandelonitrile (20 mU/mg, k(cat)/K(M) = 70 min(-1)M(-1)). This variant also catalyzed the reverse reaction, formation of mandelonitrile with low enantioselectivity: 20% ee (S), E = 1.5. The specificity constant for the lysis of mandelontrile is 13,000-fold faster than the uncatalyzed reaction and only 1300-fold less efficient (k(cat/)K(M)) than hydroxynitrile lyase from rubber tree.

Protein structure databases

Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses and schematic diagrams relating to its 3D structure and biological function. Also of great interest are the databases that classify 3D structures by their folds as these can reveal evolutionary relationships which may be hard to detect from sequence comparison alone. Related to these are the numerous servers that compare folds-particularly useful for newly solved structures, and especially those of unknown function. Beyond these there are a vast number of databases for the most specialized user, dealing with specific families, diseases, structural features and so on.

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Protein domain assignment from the recurrence of locally similar structures

Domains are basic units of protein structure and essential for exploring protein fold space and structure evolution. With the structural genomics initiative, the number of protein structures in the Protein Databank (PDB) is increasing dramatically and domain assignments need to be done automatically. Most existing structural domain assignment programs define domains using the compactness of the domains and/or the number and strength of intra-domain versus inter-domain contacts. Here we present a different approach based on the recurrence of locally similar structural pieces (LSSPs) found by one-against-all structure comparisons with a dataset of 6373 protein chains from the PDB. Residues of the query protein are clustered using LSSPs via three different procedures to define domains. This approach gives results that are comparable to several existing programs that use geometrical and other structural information explicitly. Remarkably, most of the proteins that contribute the LSSPs defining a domain do not themselves contain the domain of interest. This study shows that domains can be defined by a collection of relatively small locally similar structural pieces containing, on average, four secondary structure elements. In addition, it indicates that domains are indeed made of recurrent small structural pieces that are used to build protein structures of many different folds as suggested by recent studies.

A hybrid structural model of the complete Brugia malayi cytoplasmic asparaginyl-tRNA synthetase

Aminoacyl-tRNA synthetases are validated molecular targets for anti-infective drug discovery because of their essentiality in protein synthesis. Thanks to genome sequencing, it is now possible to systematically study aminoacyl-tRNA synthetases from human eukaryotic parasites as putative targets for novel drug discovery. As part of a program targeting class IIb asparaginyl-tRNA synthetases (AsnRS) from the parasitic nematode Brugia malayi for anti-filarial drugs, we report the complete structure of a eukaryotic AsnRS. Metazoan and fungal AsnRS differ from their bacterial homologues by the addition of a conserved N-terminal extension of about 110 residues whose structure we have determined by solution NMR for the B. malayi enzyme. In addition, we solved by X-ray crystallography a series of structures of the catalytically active N-terminally truncated enzyme (residues 112-548), allowing the structural basis for the mechanism of asparagine activation to be elucidated. The N-terminal domain contains a structured region with a novel fold featuring a lysine-rich helix that is shown by NMR to interact with tRNA. This is connected by an unstructured tether to the remainder of the enzyme, which is highly similar to the known structure of bacterial AsnRS. These data enable a model of the complete AsnRS-tRNA complex to be constructed.

Ceramide synthases in mammalians, worms, and insects: emerging schemes

The ceramide synthase (CerS) gene family comprises a group of highly conserved transmembrane proteins, which are found in all studied eukaryotes. The key feature of the CerS proteins is their role in ceramide synthase activity. Therefore, their original name ‘longevity assurance gene (Lass) homologs’, after the founding member, the yeast longevity assurance gene lag1, was altered to ‘CerS’. All CerS have high sequence similarity in a domain called LAG1 motif and a subset of CerS proteins is predicted to contain a Homeobox (Hox) domain. These domains could be the key to the multiple roles CerS have. CerS proteins play a role in diverse biological processes such as proliferation, differentiation, apoptosis, stress response, cancer, and neurodegeneration. In this review, we focus on CerS structure and biological function with emphasis of biological functions in the widely used model systems Caenorhabditis elegans and Drosophila melanogaster. Also, we focus on the accumulating data suggesting a role for CerS in lipid homeostasis.

Identification of sequence mutations affecting hemagglutinin specificity to sialic acid receptor in influenza A virus subtypes

The attachment of the hemagglutinin protein of the H1N1 subtype of the pandemic influenza A virus to the sialic acid receptor Sia(α2-6)Gal has contributed to the ability of the virus to replicate in the human body and transmit among humans. In view of the pandemic caused by the replication and transmission of the H1N1 virus, more studies on the specificity of hemagglutinin towards sialic acid and how it affects the replication and transmission ability of this virus among humans are needed. In this study, we have applied sequence, structural and functional analyses to the hemagglutinin protein of the pandemic H1N1 virus, with the aim of identifying amino acid mutation patterns that affect its specificity to sialic acid. We have also employed a molecular docking method to evaluate the complex formed between hemagglutinin protein and the sialic acid receptor. Based on our results, we suggest two possible mutation patterns, namely (1) positions 190 and 225 from glutamic acid and glycine to aspartic acid (E190D in A/Brevig Mission/1/18 (H1N1), A/New York/1/18(H1N1) and A/South Carolina/1/1918(H1N1) and G225D in A/South Carolina/1/1918(H1N1), A/South Carolina/1/1918(H1N1), and A/Puerto Rico/8/34(H1N1)), and (2) positions 226 and 228 from glutamine and glycine to leucine and serine, respectively (Q226L and G228S in A/Guiyang/1/1957(H2N2), A/Kayano/57(H2N2), A/Aichi/2/1968(H3N2), A/Hong Kong/1/1968(H3N2) and A/Memphis/1/68(H3N2)) that can potentially contribute to the specificity of hemagglutinin to Sia(α2-6)Gal, thereby enabling the replication and transmission of virus within and among humans.

PSS-SQL: protein secondary structure - structured query language

Secondary structure representation of proteins provides important information regarding protein general construction and shape. This representation is often used in protein similarity searching. Since existing commercial database management systems do not offer integrated exploration methods for biological data e.g. at the level of the SQL language, the structural similarity searching is usually performed by external tools. In the paper, we present our newly developed PSS-SQL language, which allows searching a database in order to identify proteins having secondary structure similar to the structure specified by the user in a PSS-SQL query. Therefore, we provide a simple and declarative language for protein structure similarity searching.

Structure of a zinc-binding domain in the Junin virus envelope glycoprotein

Arenaviruses cause acute hemorrhagic fevers with high mortality. Entry of the virus into the host cell is mediated by the viral envelope glycoprotein, GPC. In contrast to other class I viral envelope glycoproteins, the mature GPC complex contains a cleaved stable signal peptide (SSP) in addition to the canonical receptor-binding (G1) and transmembrane fusion (G2) subunits. SSP is critical for intracellular transport of the GPC complex to the cell surface and for its membrane-fusion activity. Previous studies have suggested that SSP is retained in GPC through interaction with a zinc-binding domain (ZBD) in the cytoplasmic tail of G2. Here we used NMR spectroscopy to determine the structure of Junín virus (JUNV) ZBD (G2 residues 445-485) and investigate its interaction with a conserved Cys residue (Cys-57) in SSP. We show that JUNV ZBD displays a novel fold containing two zinc ions. One zinc ion is coordinated by His-447, His-449, Cys-455, and His-485. The second zinc ion is coordinated by His-459, Cys-467, and Cys-469 and readily accepts Cys-57 from SSP as the fourth ligand. Our studies describe the structural basis for retention of the unique SSP subunit and suggest a mechanism whereby SSP is positioned in the GPC complex to modulate pH-dependent membrane fusion.

Engineered split in Pfu DNA polymerase fingers domain improves incorporation of nucleotide gamma-phosphate derivative

Using compartmentalized self-replication (CSR), we evolved a version of Pyrococcus furiosus (Pfu) DNA polymerase that tolerates modification of the γ-phosphate of an incoming nucleotide. A Q484R mutation in α-helix P of the fingers domain, coupled with an unintended translational termination-reinitiation (split) near the finger tip, dramatically improve incorporation of a bulky γ-phosphate-O-linker-dabcyl substituent. Whether synthesized by coupled translation from a bicistronic (−1 frameshift) clone, or reconstituted from separately expressed and purified fragments, split Pfu mutant behaves identically to wild-type DNA polymerase with respect to chromatographic behavior, steady-state kinetic parameters (for dCTP), and PCR performance. Although naturally-occurring splits have been identified previously in the finger tip region of T4 gp43 variants, this is the first time a split (in combination with a point mutation) has been shown to broaden substrate utilization. Moreover, this latest example of a split hyperthermophilic archaeal DNA polymerase further illustrates the modular nature of the Family B DNA polymerase structure.