Cap Domain Research Articles

MD Simulation Investigation on the Binding Process of Smoke-Derived Germination Stimulants to Its Receptor.

Karrikins (KARs) are a class of smoke-derived seed germination stimulants with great significance in both agriculture and plant biology. By means of direct binding to the receptor protein KAI2, the compounds can initiate the KAR signal transduction pathway, hence triggering germination of the dormant seeds in the soil. In the research, several molecular dynamics (MD) simulation techniques were properly integrated to investigate the binding process of KAR1 to KAI2 and reveal the details of the whole binding event. The calculated binding free energy, -7.00 kcal/mol, is in good agreement with the experimental measurement, -6.83 kcal/mol. The obtained PMF profile indicates the existence of three intermediate states in the binding process. The analysis of the simulation trajectories demonstrates that, in the intermediate structures, KAR1 is stabilized by some hydrophobic residues (Phe26, Phe134, Leu142, Trp153, Phe157, Leu160, Phe194), along with several bridging water molecules, and meanwhile, the significant shifting occurs in the local conformation of the protein as the ligand's binding. A series of the residues (Gln141-Phe157) on the so-called "cap domain" are proposed to be responsible for capturing the ligand at the initial stage of the binding. Besides, the changes of the ligand's poses are also quantitatively characterized by the proper choice of the coordinate system. Our work will contribute to the more penetrating understanding of the ligand binding process and the receptor affinity difference between several members in the KAR family and help design new, more effective germination stimulants.

A Recurrent Motif: Diversity and Evolution of ShKT Domain Containing Proteins in the Vampire Snail Cumia reticulata.

Proteins of the ShK superfamily are characterized by a small conserved domain (ShKT), first discovered in small venom peptides produced by sea anemones, and acting as specific inhibitors of voltage-dependent and calcium-activated K+ channels. The ShK superfamily includes both small toxic peptides and larger multifunctional proteins with various functions. ShK toxins are often important components of animal venoms, where they perform different biological functions including neurotoxic and immunosuppressive effects. Given their high specificity and effectiveness, they are currently regarded as promising pharmacological lead compounds for the treatment of autoimmune diseases. Here, we report on the molecular analysis of ShKT domain containing proteins produced by the Mediterranean vampire snail Cumia reticulata, an ectoparasitic gastropod that feeds on benthic fishes. The high specificity of expression of most ShK transcripts in salivary glands identifies them as relevant components of C. reticulata venom. These ShK proteins display various structural architectures, being produced either as single-domain secretory peptides, or as larger proteins combining the ShKT with M12 or CAP domains. Both ShKT-containing genes and their internal ShKT domains undergo frequent duplication events in C. reticulata, ensuring a high level of variability that is likely to play a role in increasing the range of their potential molecular targets.

Zinc binding regulates amyloid-like aggregation of GAPR-1.

Members of the CAP superfamily (Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1 proteins) are characterized by the presence of a CAP domain that is defined by four sequence motifs and a highly conserved tertiary structure. A common structure–function relationship for this domain is hitherto unknown. A characteristic of several CAP proteins is their formation of amyloid-like structures in the presence of lipids. Here we investigate the structural modulation of Golgi-Associated plant Pathogenesis Related protein 1 (GAPR-1) by known interactors of the CAP domain, preceding amyloid-like aggregation. Using isothermal titration calorimetry (ITC), we demonstrate that GAPR-1 binds zinc ions. Zn2+ binding causes a slight but significant conformational change as revealed by CD, tryptophan fluorescence, and trypsin digestion. The Zn2+-induced conformational change was required for the formation of GAPR-1 oligomers and amyloid-like assemblies in the presence of heparin, as shown by ThT fluorescence and TEM. Molecular dynamics simulations show binding of Zn2+ to His54 and His103. Mutation of these two highly conserved residues resulted in strongly diminished amyloid-like aggregation. Finally, we show that proteins from the cysteine-rich secretory protein (CRISP) subfamily are also able to form ThT-positive structures in vitro in a heparin- and Zn2+-dependent manner, suggesting that oligomerization regulated by metal ions could be a common structural property of the CAP domain.

Haematological Characterisation of Mice with Piezo1 Gain-Of-Function Mutation

Piezo1 proteins assemble as trimers to form mechanically-activated non-selective cationic channels. In physiology, their role as mechanosensors is critical to vascular development and red blood cell volume regulation. Mutations in Piezo1 are associated with two diseases which share overlapping features, despite opposing effects on the protein. Loss of function mutations are linked to lymphatic dysplasia; whilst gain of function mutations are connected to dehydrated stomatocytosis (DHS), a form of anaemia. Gain-of-function mutations occurring in the extracellular cap domain of the protein have been linked to DHS. To test whether such mutations are sufficient to cause DHS, we generated the equivalent of a human DHS mutation in mice using CRISPR/Cas-9 technology, mirroring the genotype observed in DHS patients. Mice homozygous for the mutation were viable with normal Mendelian inheritance and body weight. Haematological analysis revealed that the mice had characteristics of DHS, with an anaemia phenotype and the presence of stomatocytes in blood smears. The data suggest that point mutation in the Piezo1 cap is sufficient to cause anaemia and that the mutation affects murine Piezo1 similarly to human Piezo1. Further studies will investigate if the mutation has wider implications for other non-haematological systems because of the suggested broad importance of Piezo1 in mammalian physiology. Support by the Wellcome Trust and a British Heart Foundation PhD Studentship to EE.

How does the mutation in the cap domain of methylcobalamin-dependent methionine synthase influence the photoactivation of the Co-C bond?

Methionine synthase (MetH) is a methylcobalamin (MeCbl)-dependent mammalian enzyme which plays a critical role in carrying out the transfer of a methyl group from methyl tetrahydrofolate to homocysteine to generate methionine and tetrahydrofolate. This catalytic cycle proceeds via cleavage of a Co-C bond which is formally heterolytic. This cleavage results in a structural change in the MeCbl cofactor bound to an enzyme. Unlike the native catalysis, upon photoexcitation, the Co-C bond in MeCbl-bound MetH generates the Co(ii)/CH3 radical pairs (RPs). Protein residues of the cap domain, particularly phenylalanine708 (F708) and leucine 715 (L715), which surrounds the upper face of the MeCbl cofactor, inhibit the photolysis of MeCbl by caging the CH3 radical and inducing the geminate recombination of the Co(ii)/CH3 RP. A molecular-level understanding of these effects requires a detailed investigation of the low-lying electronic states. Toward this, we have mutated the F708 residue with alanine (A708) and constructed the potential energy surfaces (PESs) for the low-lying S1 electronic state using a combined quantum mechanics/molecular mechanics (QM/MM) approach. The S1 PESs for the wild-type (WT) and mutant enzymes are the result of crossing of two electronic states, namely metal-to-ligand charge transfer (MLCT) and ligand field (LF) states, indicated by a seam. It is shown that the topologies of the S1 PESs are significantly modulated by introducing a mutation at the F708 position. Specifically, for the WT enzyme, the energy barrier of photoreaction and the energy difference between MLCT and LF minima are markedly higher than those of its mutant counterpart. Moreover, mutation influences the photoactivation of the Co-C bond in enzyme-bound MeCbl by decreasing the rate of geminate recombination and altering the rate of radical pair formation. This theoretical insight was also compared with transient absorption spectroscopic (TAS) studies which are in good agreement with the present findings.

Enhanced protective immune response to PCV2 adenovirus vaccine by fusion expression of Cap protein with InvC in pigs.

The major immunogenic protein capsid (Cap) of porcine circovirus type 2 (PCV2) is critical to induce neutralizing antibodies and protective immune response against PCV2 infection. This study was conducted to investigate the immune response of recombinant adenovirus expressing PCV2b Cap and C-terminal domain of Yersinia pseudotuberculosis invasin (Cap-InvC) fusion protein in pigs. The recombinant adenovirus rAd-Cap-InvC, rAd-Cap and rAd were generated and used to immunize pigs. The phosphate-buffered saline was used as negative control. The specific antibodies levels in rAd-Cap-InvC and ZJ/C-strain vaccine groups were higher than that of rAd-Cap group (p < 0.05), and the neutralization antibody titer in rAd-Cap-InvC group was significantly higher than those of other groups during 21–42 days post-immunization (DPI). Moreover, lymphocyte proliferative level, interferon-γ and interleukin-13 levels in rAd-Cap-InvC group were increased compared to rAd-Cap group (p < 0.05). After virulent challenge, viruses were not detected from the blood samples in rAd-Cap-InvC and ZJ/C-strain vaccine groups after 49 DPI. And the respiratory symptom, rectal temperature, lung lesion and lymph node lesion were minimal and similar in the ZJ/C-strain and rAd-Cap-InVC groups. In conclusion, our results demonstrated that rAd-Cap-InvC was more efficiently to stimulate the production of antibody and protect pigs from PCV2 infection. We inferred that InvC is a good candidate gene for further development and application of PCV2 genetic engineering vaccine.

New Thermophilic α/β Class Epoxide Hydrolases Found in Metagenomes From Hot Environments.

Two novel epoxide hydrolases (EHs), Sibe-EH and CH65-EH, were identified in the metagenomes of samples collected in hot springs in Russia and China, respectively. The two α/β hydrolase superfamily fold enzymes were cloned, over-expressed in Escherichia coli, purified and characterized. The new EHs were active toward a broad range of substrates, and in particular, Sibe-EH was excellent in the desymmetrization of cis-2,3-epoxybutane producing the (2R,3R)-diol product with ee exceeding 99%. Interestingly these enzymes also hydrolyse (4R)-limonene-1,2-epoxide with Sibe-EH being specific for the trans isomer. The Sibe-EH is a monomer in solution whereas the CH65-EH is a dimer. Both enzymes showed high melting temperatures with the CH65-EH being the highest at 85°C retaining 80% of its initial activity after 3 h thermal treatment at 70°C making it the most thermal tolerant wild type epoxide hydrolase described. The Sibe-EH and CH65-EH have been crystallized and their structures determined to high resolution, 1.6 and 1.4 Å, respectively. The CH65-EH enzyme forms a dimer via its cap domains with different relative orientation of the monomers compared to previously described EHs. The entrance to the active site cavity is located in a different position in CH65-EH and Sibe-EH in relation to other known bacterial and mammalian EHs.

Intermolecular ionic interactions serve as a possible switch for stem release in the staphylococcal bi-component toxin for β-barrel pore assembly

The β-strand stem release system of staphylococcal β-barrel pore-forming toxin γ-hemolysin was investigated. Mutations at K15 and R16 in the cap domain of Hlg2 decreased hemolytic activity more markedly than their effect on erythrocyte binding. In addition, D122N mutation of LukF prestem lost the activity with Hlg2 R16A, indicating that electrostatic interactions between residues in the Hlg2 cap and prestem of adjacent LukF in the ring-shaped complex might serve as a switch for stem release.

Theoretical Study on Zearalenol Compounds Binding with Wild Type Zearalenone Hydrolase and V153H Mutant

Zearalenone hydrolase (ZHD) is the only reported α/β-hydrolase that can detoxify zearalenone (ZEN). ZHD has demonstrated its potential as a treatment for ZEN contamination that will not result in damage to cereal crops. Recent researches have shown that the V153H mutant ZHD increased the specific activity against α-ZOL, but decreased its specific activity to β-ZOL. To understand whyV153H mutation showed catalytic specificity for α-ZOL, four molecular dynamics simulations combining with protein network analysis for wild type ZHD α-ZOL, ZHD β-ZOL, V153H α-ZOL, and V153H β-ZOL complexes were performed using Gromacs software. Our theoretical results indicated that the V153H mutant could cause a conformational switch at the cap domain (residues Gly161–Thr190) to affect the relative position catalytic residue (H242). Protein network analysis illustrated that the V153H mutation enhanced the communication with the whole protein and residues with high betweenness in the four complexes, which were primarily assembled in the cap domain and residues Met241 to Tyr245 regions. In addition, the existence of α-ZOL binding to V153H mutation enlarged the distance from the OAE atom in α-ZOL to the NE2 atom in His242, which prompted the side chain of H242 to the position with catalytic activity, thereby increasing the activity of V153H on the α-ZOL. Furthermore, α-ZOL could easily form a right attack angle and attack distance in the ZHD and α-ZOL complex to guarantee catalytic reaction. The alanine scanning results indicated that modifications of the residues in the cap domain produced significant changes in the binding affinity for α-ZOL and β-ZOL. Our results may provide useful theoretical evidence for the mechanism underlying the catalytic specificity of ZHD.

Structural investigation of the enantioselectivity and thermostability mechanisms of esterase RhEst1

The esterase RhEst1 can catalyze the asymmetric hydrolysis of ethyl (±)-2,2-dimethylcyclopropane carboxylate (DmCpCe), yielding a pharmaceutically relevant (S)-carboxylic acid. A triple mutant RhEst1A147I/V148F/G254A showed a 5-fold increase in the catalytic activity but a significant decrease in the enantioselectivity. Further optimization studies led to a new enzyme with an additional A143T mutation, which showed both increased catalytic activity and recovered enantioselectivity as well as improved thermostability. To reveal the detailed structural mechanisms for these improved properties, we performed all-atom molecular dynamics simulations on the wild type and two mutants A147I/V148F/G254A and A143T/A147I/V148F/G254A RhEst1, in complex with R-DmCpCe and S-DmCpCe substrates, respectively. The structural stability of the enzyme variants was investigated with the residue interaction network analysis. In RhEst1M2, S-DmCpCe was observed to adopt a more “activated” conformation than R-DmCpCe, with the active site residues better prearranged for the reaction, leading to the improved enantioselectivity towards S-DmCpCe. The mutations in the two mutants, especially A143T, could lead to different motion patterns in the cap domain, thus affecting the structure of the substrate entrance tunnel. The residue interaction networks analysis showed an increased number of interactions in RhEst1M1 and RhEst1M2 as compared to the wild type enzyme, especially the π-π stacking interactions between Phe148 and the nearby residues, providing an explanation for the increased thermostability of the two mutant enzymes observed experimentally. Our work provides essential molecular insights into the substrate binding, enantioselectivity and structural stability of esterase RhEst1, which will facilitate the development of more efficient RhEst1 variants for pharmaceutical applications.

Qualitative Profiling of the Humoral Immune Response Elicited by rVSV-ΔG-EBOV-GP Using a Systems Serology Assay, Domain Programmable Arrays

Development of an effective vaccine became a worldwide priority after the devastating 2013-2016 Ebola disease outbreak. To qualitatively profile the humoral response against advanced filovirus vaccine candidates, we developed Domain Programmable Arrays (DPA), a systems serology platform to identify epitopes targeted after vaccination or filovirus infection. We optimized the assay using a panel of well-characterized monoclonal antibodies. After optimization, we utilized the system to longitudinally characterize the immunoglobulin (Ig) isotype-specific responses in non-human primates vaccinated with rVSV-ΔG-EBOV-glycoprotein (GP). Strikingly, we observed that, although the IgM response was directed against epitopes over the whole GP, the IgG and IgA responses were almost exclusively directed against the mucin-like domain (MLD) of the glycan cap. Further research will be needed to characterize this possible biased IgG and IgA response toward the MLD, but the results corroborate that DPA is a valuable tool to qualitatively measure the humoral response after vaccination.

Mechanism of Substrate Recognition and Catalysis of the Haloalkanoic Acid Dehalogenase Family Member α-Phosphoglucomutase

α-Phosphoglucomutase (αPGM), in its phosphorylated state, catalyzes the interconversion of α-d-glucose 1-phosphate and α-d-glucose 6-phosphate. The αPGM of Lactococcus lactis is a type C2B member of the haloalkanoic acid dehalogenase (HAD) enzyme family and is comprised of a Rossmann-fold catalytic domain and inserted α/β-fold cap domain. The active site is formed at the domain-domain interface. Herein, we report the results from a kinetic-based study of L. lactis αPGM catalysis, which demonstrate enzyme activation by autocatalyzed phosphorylation of Asp8 with αG1P, the intermediacy of αG1,6bisP in the phospho Ll-αPGM-catalyzed conversion of αG1P to G6P, and the reorientation of the αG1,6bisP intermediate via dissociation to solvent and rebinding. In order to provide insight into the structural determinants of L. lactis αPGM substrate recognition and catalysis, metal cofactor and substrate specificities were determined as were the contributions made by active-site residues toward catalytic efficiency. Lastly, the structure and catalytic mechanism of L. lactis αPGM are compared with those of HAD family phosphomutases L. lactis β-phosphoglucomutase and eukayotic α-phosphomannomutase to provide insight into the evolution of phosphohexomutases from HAD family phosphatases.

The MRX complex regulates Exo1 resection activity by altering DNA end structure.

Homologous recombination is triggered by nucleolytic degradation (resection) of DNA double-strand breaks (DSBs). DSB resection requires the Mre11-Rad50-Xrs2 (MRX) complex, which promotes the activity of Exo1 nuclease through a poorly understood mechanism. Here, we describe the Mre11-R10T mutant variant that accelerates DSB resection compared to wild-type Mre11 by potentiating Exo1-mediated processing. This increased Exo1 resection activity leads to a decreased association of the Ku complex to DSBs and an enhanced DSB resection in G1, indicating that Exo1 has a direct function in preventing Ku association with DSBs. Molecular dynamics simulations show that rotation of the Mre11 capping domains is able to induce unwinding of double-strand DNA (dsDNA). The R10T substitution causes altered orientation of the Mre11 capping domain that leads to persistent melting of the dsDNA end. We propose that MRX creates a specific DNA end structure that promotes Exo1 resection activity by facilitating the persistence of this nuclease on the DSB ends, uncovering a novel MRX function in DSB resection.

Bifurcation of Mixed Mode Reaction–Diffusion Patterns in Spherical Caps

We study pattern formation in a chemical reaction–diffusion system of partial differential equations in spherical cap domains. For certain critical values of parameters corresponding to cap flatness, cap radius, and chemical precursor concentrations, the unpatterned solution is unstable to two different linear normal modes. We use center manifold and normal form reductions to analyze the existence and stability of pure and mixed modes of nonlinear patterned solutions of the reaction–diffusion system, for parameters with two cases of critical values. In one case, the system reduces to a well known example of mode interaction. In the other case, the mode interaction is new, due to very small quadratic terms in the normal form.

Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site.

Haloalkane dehalogenases catalyze the hydrolysis of halogen-carbon bonds in organic halogenated compounds and as such are of great utility as biocatalysts. The crystal structures of the haloalkane dehalogenase DhlA from the bacterium from Xanthobacter autotrophicus GJ10, specifically adapted for the conversion of the small 1,2-dichloroethane (DCE) molecule, display the smallest catalytic site (110 Å3) within this enzyme family. However, during a substrate-specificity screening, we noted that DhlA can catalyze the conversion of far bulkier substrates, such as the 4-(bromomethyl)-6,7-dimethoxy-coumarin (220 Å3). This large substrate cannot bind to DhlA without conformational alterations. These conformational changes have been previously inferred from kinetic analysis, but their structural basis has not been understood. Using molecular dynamic simulations, we demonstrate here the intrinsic flexibility of part of the cap domain that allows DhlA to accommodate bulky substrates. The simulations displayed two routes for transport of substrates to the active site, one of which requires the conformational change and is likely the route for bulky substrates. These results provide insights into the structure-dynamics function relationships in enzymes with deeply buried active sites. Moreover, understanding the structural basis for the molecular adaptation of DhlA to 1,2-dichloroethane introduced into the biosphere during the industrial revolution provides a valuable lesson in enzyme design by nature.

Using M. marinum T6PP as a Model for M. tuberculosis Inhibitor Design

Trehalose-6-phosphate phosphatase (T6PP) is a member of the haloalkanoic acid dehalogenase superfamily (HADSF) acting upon trehalose 6-phosphate, an intermediate in the pathway by which glucose 6-phosphate is converted to trehalose (1). The gene encoding T6PP, otsB, is conserved among bacterial pathogens, such as Mycobacterium tuberculosis, but absent in mammalian species. Bacterial pathogens of the Mycolata taxon utilize trehalose to synthesize cord factor, a mycolic acid-derived membrane glycolipid enabling toxicity, pathogenicity, and phagocyte survival (2). The otsB-knockout of M. tuberculosis precludes pathogen growth in vitro and virulence in a mouse model (2); thus, T6PP inhibitors are desired as therapeutics. Due to the 76% sequence identity between M. marinum and M. tuberculosis T6PP, our study investigates the molecular structure of T6PP from the model organism M. marinum in order to understand the binding determinants of the M. tuberculosis ortholog. Toward this goal, we have determined the unliganded structure of M. marinum to 1.97 □ resolution with a magnesium ion cofactor. The structure consists of 3 domains: the N-terminal, Rossmann-like core and cap domains. Like many other unliganded T6PP structures, the active site, located at cap-core interface, is exposed to solvent and is not in a conformation competent to bind substrate. However, comparison of the individual domains with M. tuberculosis T6PP results in an RMSD score of 0.64, 0.60, and 0.85 for the N-terminal, core and cap domains, respectively. We have measured the steady-state kinetic constants of M. marinum T6PP as kcat of 13 s−1 and a Km of 150 μM, which are comparable to those from the M. tuberculosis enzyme (kcat of 10 s−1 and Km of 500 μM) (3). Together these data confirm that the M. marinum enzyme is a model for structural and kinetic studies. To date, collaboration with The Scripps Research Institute facilitated the discovery of two T6PP inhibitors: clinically employed compounds Closantel and Cephalosporin C. We have determined a Ki for M. marinum T6PP of 39 μM in the presence of Cephalosporin C. Based on clinical data reporting the usage of the drug for tuberculosis therapy (4), we postulate that Cephalosporin C inhibits T6PP by preventing cord factor synthesis and thereby bacterial pathogenicity. In the future, we seek to determine the liganded structure of M. marinum T6PP with potential inhibitors bound. Support or Funding Information This work was funded by the Arnold and Mabel Beckman Foundation and Boston University Undergraduate Research Opportunities Program. Newly determined structure of M. marinum T6PP overlaid onto known structure of M. tuberculosis T6PP. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Crystal structure of an assembly intermediate of respiratory Complex II

In approximately 10% of flavoenzymes, the flavin is covalently attached. Despite the importance of this covalent cofactor for a number of biological functions, the mechanism of covalent flavinylation is currently poorly understood. In this work, we determined the crystal structure of a captured assembly intermediate of covalent flavinylation using the Escherichia coli Complex II FrdA subunit crosslinked with its assembly factor, SdhE. Two global conformational changes in FrdA subunit were observed as compared to prior structures of the assembled Complex II protein: rotation of the capping domain, and the destabilization of two large loops proximal to the active site of the FrdA subunit. Together, these changes create a tunnel to the active site. This FrdA‐SdhE structure was used as a basis to develop a mechanism of covalent flavinylation that is supported by spectroscopic and kinetic analyses.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Mechanistic basis for the activation of plant membrane receptor kinases by SERK-family coreceptors

Plant-unique membrane receptor kinases with leucine-rich repeat ectodomains (LRR-RKs) can sense small molecule, peptide, and protein ligands. Many LRR-RKs require SERK-family coreceptor kinases for high-affinity ligand binding and receptor activation. How one coreceptor can contribute to the specific binding of distinct ligands and activation of different LRR-RKs is poorly understood. Here we quantitatively analyze the contribution of SERK3 to ligand binding and activation of the brassinosteroid receptor BRI1 and the peptide hormone receptor HAESA. We show that while the isolated receptors sense their respective ligands with drastically different binding affinities, the SERK3 ectodomain binds the ligand-associated receptors with very similar binding kinetics. We identify residues in the SERK3 N-terminal capping domain, which allow for selective steroid and peptide hormone recognition. In contrast, residues in the SERK3 LRR core form a second, constitutive receptor-coreceptor interface. Genetic analyses of protein chimera between BRI1 and SERK3 define that signaling-competent complexes are formed by receptor-coreceptor heteromerization in planta. A functional BRI1-HAESA chimera suggests that the receptor activation mechanism is conserved among different LRR-RKs, and that their signaling specificity is encoded in the kinase domain of the receptor. Our work pinpoints the relative contributions of receptor, ligand, and coreceptor to the formation and activation of SERK-dependent LRR-RK signaling complexes regulating plant growth and development.

Expansion of cap superfamily proteins in the genome of Mesocestoides corti: An extreme case of a general bilaterian trend

The CAP superfamily is a diverse group of proteins that are involved in different biological processes, yet their molecular functions are still incompletely understood. The α-β-α sandwich structure of the CAP domain is characteristic of this superfamily and several different domains may be found together with it. They are generally secreted proteins and in helminths many are secreted to the environment, and are related to the host-parasite interaction. In this work we mined cestode genomic data for members of this superfamily. Whereas in average 26 members with complete CAP domains were found in most cestodes, in Mesocestoides corti we strikingly found 271 members with complete domains, most of which show evidence of expression. We also found other truncated domains and putative pseudogenes. Interestingly, most of these genes were found in a monophyletic clade within a cestode-specific group of CAP domain containing proteins, and each cestode species has also developed independent duplications of these proteins. This pattern of extensive independent duplications can also be found in other parasitic and free-living flatworms, as well as in other metazoan phyla. Within the M. corti specific expansion, several sub-clades of these proteins showed evidence of evolution under positive selection. Our results suggest that the CAP domain containing proteins of animals evolve through a “birth and death” mechanism, and that different environmental pressures may drive this evolution in different species. In the case of helminth parasites, this could be related to the interaction between the parasite and the host, including mechanisms to evade and modulate the host immune system.

Crystal structure of bacterial succinate:quinone oxidoreductase flavoprotein SdhA in complex with its assembly factor SdhE

Succinate:quinone oxidoreductase (SQR) functions in energy metabolism, coupling the tricarboxylic acid cycle and electron transport chain in bacteria and mitochondria. The biogenesis of flavinylated SdhA, the catalytic subunit of SQR, is assisted by a highly conserved assembly factor termed SdhE in bacteria via an unknown mechanism. By using X-ray crystallography, we have solved the structure of Escherichia coli SdhE in complex with SdhA to 2.15-Å resolution. Our structure shows that SdhE makes a direct interaction with the flavin adenine dinucleotide-linked residue His45 in SdhA and maintains the capping domain of SdhA in an "open" conformation. This displaces the catalytic residues of the succinate dehydrogenase active site by as much as 9.0 Å compared with SdhA in the assembled SQR complex. These data suggest that bacterial SdhE proteins, and their mitochondrial homologs, are assembly chaperones that constrain the conformation of SdhA to facilitate efficient flavinylation while regulating succinate dehydrogenase activity for productive biogenesis of SQR.