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Microbial electrosynthesis is an emerging green technology that explores the capability of a particular group of microorganisms to drive their metabolism toward the production of hydrogen or value-added chemicals from electrons supplied by electrode surfaces. The cytochrome PccH showed the largest increase in transcription when electrons are supplied to Geobacter sulfurreducens biofilms. Gene knock-out experiments have shown that the electron transfer toward G. sulfurreducens cells was completely inhibited by the deletion of the gene encoding for cytochrome PccH. This identifies a crucial role for this protein in G. sulfurreducens microbial electrosynthesis mechanisms, which are currently unknown. In this work, we present the backbone (H, C and N) and heme assignment for PccH in the oxidized state. The data obtained paves the way to identify and structurally map the molecular interaction regions between the cytochrome PccH and its physiological redox partners.

An NMR vision on Biomolecular interactions

TACC3 is a centrosomal adaptor protein that plays important roles during mitotic spindle assembly. It interacts with chTOG/XMAP215, which catalyzes the addition of tubulin dimers during microtubule growth. A 3D coiled-coil model for this interaction is available but the structural details are not well described. To characterize this interaction at atomic resolution, we have designed a simplified version of the system based on small peptides. Four different peptides have been studied by circular dichroism and nuclear magnetic resonance both singly and in all possible combinations; namely, five peptide pairs and two trios. In cosolvents, all single peptides tend to adopt helical conformations resembling those of the full-length protein. However, neither the single peptides nor pairs of peptides form coiled coils. We show that the simultaneous presence of all preformed helices is a prerequisite for binding. The simplest 3D model for the interaction, based on the NMR results, is proposed. Interestingly, the peptide's structure remains unaffected by mutations at essential positions for TACC3 activity. This suggests that the lack of interaction of this TACC3 mutant with XMAP does not correlate with changes in the protein structure and that specific interactions are likely responsible for the interaction and stability of the complex.

Despite the growing number of carbohydrate-binding modules (CBMs) that are being uncovered, information on the structural determinants for the sugar-binding regions at atomic resolution is scarce. It is widely accepted that aromatic and H-bonding interactions govern these processes, and reported simulations and theoretical calculations are valuable tools to quantify and understand these interactions. We present here a computational model derived from experimental data that provide a unique atomistic picture of an uncharacterized binding mode of laminarin to the CBM family 43. The present study, which is among the first describing an isolated CBM with the bound carbohydrate, is complemented with quantum mechanical calculations. This allows us to attribute certain experimental observations (binding affinities) to key interactions (H-bonds and aromatic stacking), on the basis of NMR-driven docking structure.

Gene knock-out studies on Geobacter sulfurreducens cells showed that the outer membrane-associated monoheme cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) and U(VI). In addition, microarray analysis of an OmcF-deficient mutant revealed that many of the genes with decreased transcript level were those whose expression is up-regulated in cells grown with a graphite electrode as electron acceptor, suggesting that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electricity production by G. sulfurreducens in microbial fuel cells. N,C–labeled OmcF was produced and NMR spectroscopy was used to determine the solution structure of the protein in the fully reduced state and the pH-dependent conformational changes. In addition, N relaxation NMR experiments were used to characterize the overall and internal backbone dynamics of OmcF. The structure obtained is well-defined, with an average pairwise root mean square deviation of 0.37 Å for the backbone atoms and 0.98 Å for all heavy atoms. For the first time a solution structure and the protein motions were determined for an outer membrane cytochrome from G. sulfurreducens, which constitutes an important step to understand the extracellular electron transfer mechanism in Geobacter cells.

The periplasmic triheme cytochrome PpcA from Geobacter sulfurreducens is highly abundant; it is the likely reservoir of electrons to the outer surface to assist the reduction of extracellular terminal acceptors; these include insoluble metal oxides in natural habitats and electrode surfaces from which electricity can be harvested. A detailed thermodynamic characterization of PpcA showed that it has an important redox-Bohr effect that might implicate the protein in e/H coupling mechanisms to sustain cellular growth. This functional mechanism requires control of both the redox state and the protonation state. In the present study, isotope-labeled PpcA was produced and the three-dimensional structure of PpcA in the oxidized form was determined by NMR. This is the first solution structure of a G. sulfurreducens cytochrome in the oxidized state. The comparison of oxidized and reduced structures revealed that the heme I axial ligand geometry changed and there were other significant changes in the segments near heme I. The pH-linked conformational rearrangements observed in the vicinity of the redox-Bohr center, both in the oxidized and reduced structures, constitute the structural basis for the differences observed in the pK values of the redox-Bohr center, providing insights into the e/H coupling molecular mechanisms driven by PpcA in G. sulfurreducens.

Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.

Apoptin is a nonstructural protein encoded by one of the three open reading frames of the chicken anemia virus genome. It has attracted a great deal of interest due to its ability to induce apoptosis in multiple transformed and malignant mammalian cell lines without affecting primary and non-transformed cells. However, the use of Apoptin as an anticancer drug is restricted by its strong tendency to aggregate. A number of methods to overcome this problem have been proposed, including transduction techniques to deliver the Apoptin gene into tumor cells, but all such methods have certain drawbacks. Here we describe that a truncated variant of Apoptin, lacking residues 1 to 43, is a soluble, non-aggregating protein that maintains most of the biological properties of wild-type Apoptin when transfected into cells. We show that the cytotoxic effect of this variant is also present when it is added exogenously to cancer cells, but not to normal cells. In addition to the interest this protein has attracted as a promising therapeutic strategy, it is also an excellent model to study the structural properties of Apoptin and how they relate to its mechanism of action.

Chol!ne-binding proteins «BPs) are ¡"volved in a wlde rage of physiological fu nctioos. CbpL 'rom 5. pneumoniae is a CHPs of 332 residues-Iong prole¡n, Jt has 3 weU-di(ferentiated domalns (onnected by linker regions thal provlde flexibility ro me general structure. The enninal dornajo ¡ndudes .ln Excalibur domaln (from extracelular calciUll1-bfnding region) af unknown sl,ucture aOO funelían, although in sorne cases these domalos have been proposed 10 be ¡nvolved in adhesion and colonlzatioo processes. Here we describe far ¡he fir.;,t time. lhe solution 3D struaure af the Excalibur domaln by using heteronudear multid lmensional NMR spectroscopy. Ir\ the absence of Ca2+. lhe NMR speclra showed thal lhe proteinexrmas a random coil or an unfolded polypeptide. Addilion of (a2+ dramatically changed the distribution and the disperslon 01 lhe NMR signals indicatlng thal the proteln was folded upon (aH bindlng. AccOfdlng 10 lrus. we have sHucturaUy c.haracterized the folded entity in the presenee of saturation eoncentrations ol Ca2+. The global lold o, the domaln shows an inrtlcate globular shape (16 )C 20)( 27 Al e~mbllng a wool balL TIle strueture has a disordered N*terminal short tan, and el globular paeked domaln containing a short u-he lical region. a calcium·binding sile. and a disordered (-terminal region. Al! Ihe residues in the OxOxDGxxCE motif are ¡nvolved in calcium binding in a (anonieal disposition. The two Cys rcsidues establish a dlsulphide bridge that connects the short a-he/leal region with the Ca-binding site. The structural details of the EXCi,llibur domain will be discussed In the context of the fulllength CbpL proteio. which i:s expecled lo rema!n slrongly anchored 10 peptidoglyean layer exposing the Excalibur domain to {he capsule o r lhe extraeellular medium

A family of triheme cytochromes from Geobacter sulfurreducens plays an important role in extracellular electron transfer. In addition to their role in electron transfer pathways, two members of this family (PpcA and PpcD) were also found to be able to couple e/H transfer through the redox Bohr effect observed in the physiological pH range, a feature not observed for cytochromes PpcB and PpcE. In attempting to understand the molecular control of the redox Bohr effect in this family of cytochromes, which is highly homologous both in amino acid sequence and structures, it was observed that residue 6 is a conserved leucine in PpcA and PpcD, whereas in the other two characterized members (PpcB and PpcE) the equivalent residue is a phenylalanine. To determine the role of this residue located close to the redox Bohr center, we replaced Leu in PpcA with Phe and determined the redox properties of the mutant, as well as its solution structure in the fully reduced state. In contrast with the native form, the mutant PpcAL6F is not able to couple the e/H pathway. We carried out the reverse mutation in PpcB and PpcE (i.e., replacing Phe in these two proteins by leucine) and the mutated proteins showed an increased redox Bohr effect. The results clearly establish the role of residue 6 in the control of the redox Bohr effect in this family of cytochromes, a feature that could enable the rational design of G. sulfurreducens strains that carry mutant cytochromes with an optimal redox Bohr effect that would be suitable for various biotechnological applications.

Coordination polymers and metal-organic frameworks are appealing as synthetic hosts for mediating chemical reactions. Here we report the preparation of a mesoscopic metal-organic structure based on single-layer assembly of aluminium chains and organic alkylaryl spacers. The material markedly accelerates condensation reactions in water in the absence of acid or base catalyst, as well as organocatalytic Michael-type reactions that also show superior enantioselectivity when comparing with the host-free transformation. The mesoscopic phase of the solid allows for easy diffusion of products and the catalytic solid is recycled and reused. Saturation transfer difference and two-dimensional (1)H nuclear Overhauser effect NOESY NMR spectroscopy show that non-covalent interactions are operative in these host-guest systems that account for substrate activation. The mesoscopic character of the host, its hydrophobicity and chemical stability in water, launch this material as a highly attractive supramolecular catalyst to facilitate (asymmetric) transformations under more environmentally friendly conditions.

The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus.

The I27 module from human cardiac titin has become a standard in protein nanomechanics. A proline-scanning study of its ¿mechanical clamp¿ found three mechanically hypomorphic mutants and a paradoxically hypermorphic one (Y9P). Both types of mutants have been commonly used as substrates of several protein unfoldase machineries in studies relating protein mechanostability to translocation or degradation rates. Using AFM-based single-molecule force spectroscopy, polyprotein engineering and steered molecular dynamics simulations we show that, unexpectedly, the mechanostability of the Y9P variant is comparable to the wild type. Furthermore, the NMR analysis of homomeric polyproteins of this variant suggests that these constructs may induce slight structural perturbations in the monomer, and enables us to explain some minor differences in this variant¿s properties; namely the abolishment of the mechanical unfolding intermediate and a reduced thermal stability. Our results clarify a previously reported paradoxical result in protein nanomechanics and contribute to refine our toolbox for understanding the unfolding mechanism used by translocases and degradation machines.

The mechanism by which the HIV-1 MPER epitope is recognized by the potent neutralizing antibody 10E8 at membrane interfaces remains poorly understood. To solve this problem, we have optimized a 10E8 peptide epitope and analyzed the structure and binding activities of the antibody in membrane and membrane-like environments. The X-ray crystal structure of the Fab-peptide complex in detergents revealed for the first time that the epitope of 10E8 comprises a continuous helix spanning the gp41 MPER/transmembrane domain junction (MPER-N-TMD; Env residues 671-687). The MPER-N-TMD helix projects beyond the tip of the heavy-chain complementarity determining region 3 loop, indicating that the antibody sits parallel to the plane of the membrane in binding the native epitope. Biophysical, biochemical and mutational analyses demonstrated that strengthening the affinity of 10E8 for the TMD helix in a membrane environment, correlated with its neutralizing potency. Our research clarifies the molecular mechanisms underlying broad neutralization of HIV-1 by 10E8, and the structure of its natural epitope. The conclusions of our research will guide future vaccine-design strategies targeting MPER.

Amyloids are ordered protein aggregates that are typically associated with neurodegenerative diseases and cognitive impairment. By contrast, the amyloid-like state of the neuronal RNA binding protein Orb2 in Drosophila was recently implicated in memory consolidation, but it remains unclear what features of this functional amyloid-like protein give rise to such diametrically opposed behaviour. Here, using an array of biophysical, cell biological and behavioural assays we have characterized the structural features of Orb2 from the monomer to the amyloid state. Surprisingly, we find that Orb2 shares many structural traits with pathological amyloids, including the intermediate toxic oligomeric species, which can be sequestered in vivo in hetero-oligomers by pathological amyloids. However, unlike pathological amyloids, Orb2 rapidly forms amyloids and its toxic intermediates are extremely transient, indicating that kinetic parameters differentiate this functional amyloid from pathological amyloids. We also observed that a well-known anti-amyloidogenic peptide interferes with long-term memory in Drosophila. These results provide structural insights into how the amyloid-like state of the Orb2 protein can stabilize memory and be nontoxic. They also provide insight into how amyloid-based diseases may affect memory processes.

CsdA cysteine desulfurase (the sulfur donor) and the CsdE sulfur acceptor are involved in biological sulfur trafficking and in iron-sulfur cluster assembly in the model bacterium Escherichia coli. CsdA and CsdE form a stable complex through a polar interface that includes CsdA Cys328 and CsdE Cys61, the two residues known to be involved in the sulfur transfer reaction. Although mechanisms for the transfer of a sulfur moiety across protein-protein interfaces have been proposed based on the IscS-IscU and IscS-TusA structures, the flexibility of the catalytic cysteine loops involved has precluded a high resolution view of the active-site geometry and chemical environment for sulfur transfer. Here, we have used a combination of X-ray crystallography, solution NMR and SAXS, isothermal calorimetry, and computational chemistry methods to unravel how CsdA provides a specific recognition platform for CsdE and how their complex organizes a composite functional reaction environment. The X-ray structures of persulfurated (CsdA) and persulfurated (CsdA-CsdE) complexes reveal the crucial roles of the conserved active-site cysteine loop and additional catalytic residues in supporting the transpersulfuration reaction. A mechanistic view of sulfur transfer across protein-protein interfaces that underpins the requirement for the conserved cysteine loop to provide electrostatic stabilization for the in-transfer sulfur atom emerges from the analysis of the persulfurated (CsdA-CsdE) complex structure.

It has been suggested that DYNLT1, a dynein light chain known to bind to various cellular and viral proteins, can function both as a molecular clamp and as a microtubule-cargo adapter. Recent data have shown that the DYNLT1 homodimer binds to two dynein intermediate chains to subsequently link cargo proteins such as the guanine nucleotide exchange factor Lfc or the small GTPases RagA and Rab3D. Although over 20 DYNLT1-interacting proteins have been reported, the exact sequence requirements that enable their association to the canonical binding groove or to the secondary site within the DYNLT1 surface are unknown. We describe herein the sequence recognition properties of the hydrophobic groove of DYNLT1 known to accommodate dynein intermediate chain. Using a pepscan approach, we have substituted each amino acid within the interacting peptide for all 20 natural amino acids and identified novel binding sequences. Our data led us to propose activin receptor IIB as a novel DYNLT1 ligand and suggest that DYNLT1 functions as a molecular dimerization engine bringing together two receptor monomers in the cytoplasmic side of the membrane. In addition, we provide evidence regarding a dual binding mode adopted by certain interacting partners such as Lfc or the parathyroid hormone receptor. Finally, we have used NMR spectroscopy to obtain the solution structure of human DYNLT1 forming a complex with dynein intermediate chain of ∼74 kDa; it is the first mammalian structure available.

Escherichia coli CsdA cysteine desulfurase (the sulfur donor) and the CsdE sulfur acceptor are involved in biological sulfur trafficking, in iron-sulfur cluster assembly, and tRNA hypermodification [1] in the model bacterium Escherichia coli. CsdA and CsdE form a stable complex through a polar interface. Although mechanisms for the transfer of a sulfur moiety across protein-protein interfaces have been proposed based on the IscS-IscU and IscS-TusA structures [2,3], the flexibility of the catalytic Cys loops involved has precluded a high resolution view of the active-site geometry and chemical environment responsible to facilitate sulfur transfer. Here, we have used a combination of X-ray crystallography, solution NMR, biophysical and computational chemistry methods to unravel how CsdA provides a specific recognition platform for CsdE and how their complex organizes a composite functional reaction environment. A mechanistic view of sulfur transfer across protein-protein interfaces emerges from the structural analysis of the CSD system.

Escherichia coli CsdA cysteine desulfurase (the sulfur donor) and the CsdE sulfur acceptor are involved in biological sulfur trafficking, in iron-sulfur cluster assembly, and tRNA hypermodification [1] in the model bacterium Escherichia coli. CsdA and CsdE form a stable complex through a polar interface. Although mechanisms for the transfer of a sulfur moiety across protein-protein interfaces have been proposed based on the IscS-IscU and IscS-TusA structures [2,3], the flexibility of the catalytic Cys loops involved has precluded a high resolution view of the active-site geometry and chemical environment responsible to facilitate sulfur transfer. Here, we have used a combination of X-ray crystallography, solution NMR, biophysical and computational chemistry methods to unravel how CsdA provides a specific recognition platform for CsdE and how their complex organizes a composite functional reaction environment. A mechanistic view of sulfur transfer across protein-protein interfaces emerges from the structuralanalysis of the CSD system

Multiheme cytochromes have been implicated in Geobacter sulfurreducens extracellular electron transfer (EET). These proteins are potential targets to improve EET and enhance bioremediation and electrical current production by G. sulfurreducens. However, the functional characterization of multiheme cytochromes is particularly complex due to the co-existence of several microstates in solution, connecting the fully reduced and fully oxidized states. Over the last decade, new strategies have been developed to characterize multiheme redox proteins functionally and structurally. These strategies were used to reveal the functional mechanism of G. sulfurreducens multiheme cytochromes and also to identify key residues in these proteins for EET. In previous studies, we set the foundations for enhancement of the EET abilities of G. sulfurreducens by characterizing a family of five triheme cytochromes (PpcA-E). These periplasmic cytochromes are implicated in electron transfer between the oxidative reactions of metabolism in the cytoplasm and the reduction of extracellular terminal electron acceptors at the cell's outer surface. The results obtained suggested that PpcA can couple e−/H+ transfer, a property that might contribute to the proton electrochemical gradient across the cytoplasmic membrane for metabolic energy production. The structural and functional properties of PpcA were characterized in detail and used for rational design of a family of 23 single site PpcA mutants. In this review, we summarize the functional characterization of the native and mutant proteins. Mutants that retain the mechanistic features of PpcA and adopt preferential e−/H+ transfer pathways at lower reduction potential values compared to the wild-type protein were selected for in vivo studies as the best candidates to increase the electron transfer rate of G. sulfurreducens. For the first time G. sulfurreducens strains have been manipulated by the introduction of mutant forms of essential proteins w

Cyclic N6-threonylcarbamoyladenosine (‘cyclic t6A’, ct6 A) is a non-thiolated hypermodification found in transfer RNAs (tRNAs) in bacteria, protists, fungi and plants. In bacteria and yeast cells ct6 A has been shown to enhance translation fidelity and efficiency of ANN codons by improving the faithful discrimination of aminoacylated tRNAs by the ribosome. To further the understanding of ct6A biology we have determined the high-resolution crystal structures of CsdL/TcdA in complex with AMP and ATP, an E1-like activating enzyme from Escherichia coli, which catalyzes the ATP-dependent dehydration of t6A to form ct6 A. CsdL/TcdA is a dimer whose structural integrity and dimer interface depend critically on strongly bound K+ and Na+ cations. By using biochemical assays and small-angle X-ray scattering we show that CsdL/TcdA can associate with tRNA with a 1:1 stoichiometry and with the proper position and orientation for the cyclization of t6A. Furthermore, we show by nuclear magnetic resonance that CsdL/TcdA engages in transient interactions with CsdA and CsdE, which, in the latter case, involve catalytically important residues. These short-lived interactions may underpin the precise channeling of sulfur atoms from cysteine to CsdL/TcdA as previously characterized. In summary, the combination of structural, biophysical and biochemical methods applied to CsdL/TcdA has afforded a more thorough understanding of how the structure of this E1-like enzyme has been fine tuned to accomplish ct6A synthesis on tRNAs while providing support for the notion that CsdA and CsdE are able to functionally interact with CsdL/TcdA.

© 2015, Springer Science+Business Media Dordrecht. Gene knockout studies on Geobacter sulfurreducens (Gs) cells showed that the outer membrane cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) citrate and U(VI) oxide. In addition, microarray analysis of OmcF-deficient mutant versus the wild-type strain revealed that many of the genes with decreased transcript level were those whose expression is upregulated in cells grown with a graphite electrode as electron acceptor. This suggests that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electrical current production by Gs in microbial fuel cells. Extracellular electron transfer processes (EET) constitute nowadays the foundations to develop biotechnological applications in biofuel production, bioremediation and bioenergy. Therefore, the structural characterization of OmcF is a fundamental step to understand the mechanisms underlying EET. Here, we report the complete assignment of the heme proton signals together with 1H, 13C and 15N backbone and side chain assignments of the OmcF, excluding the hydrophobic residues of the N-terminal predicted lipid anchor.

© 2014, Springer Science+Business Media Dordrecht. Gene knock-out studies on Geobacter sulfurreducens (Gs) cells showed that the periplasmic triheme cytochrome PpcD is involved in respiratory pathways leading to the extracellular reduction of Fe(III) and U(VI) oxides. More recently, it was also shown that the gene encoding for PpcD has higher transcript abundance when Gs cells utilize graphite electrodes as sole electron donors to reduce fumarate. This sets PpcD as the first multiheme cytochrome to be involved in Gs respiratory pathways that bridge the electron transfer between the cytoplasm and cell exterior in both directions. Nowadays, extracellular electron transfer (EET) processes are explored for several biotechnological applications, which include bioremediation, bioenergy and biofuel production. Therefore, the structural characterization of PpcD is a fundamental step to understand the mechanisms underlying EET. However, compared to non-heme proteins, the presence of numerous proton-containing groups in the redox centers presents additional challenges for protein signal assignment and structure calculation. Here, we report the complete assignment of the heme proton signals together with 1H, 13C and 15N backbone and side chain assignments of the reduced form of PpcD.

Background:Anisakiasis is a re-emerging global disease caused by consumption of raw or lightly cooked fish contaminated with L3 Anisakis larvae. This zoonotic disease is characterized by severe gastrointestinal and/or allergic symptoms which may misdiagnosed as appendicitis, gastric ulcer or other food allergies.The Anisakis allergen Ani s 5 is a protein belonging to the SXP/RAL-2 family; it is detected exclusively in nematodes. Previous studies showed that SXP/RAL-2 proteins are active antigens; however, their structure and function remain unknown.The aim of this study was to elucidate the three-dimensional structure of Ani s 5 and its main IgE and IgG4 binding regions.Methodology/Principal Findings:The tertiary structure of recombinant Ani s 5 in solution was solved by nuclear magnetic resonance. Mg2+, but not Ca2+, binding was determined by band shift using SDS-PAGE. IgE and IgG4 epitopes were elucidated by microarray immunoassay and SPOTs membranes using sera from nine Anisakis allergic patients.The tertiary structure of Ani s 5 is composed of six alpha helices (H), with a Calmodulin like fold. H3 is a long, central helix that organizes the structure, with H1 and H2 packing at its N-terminus and H4 and H5 packing at its C-terminus. The orientation of H6 is undefined. Regarding epitopes recognized by IgE and IgG4 immunoglobulins, the same eleven peptides derived from Ani s 5 were bound by both IgE and IgG4. Peptides 14 (L40-K59), 26 (A76-A95) and 35 (I103-D122) were recognized by three out of nine sera.Conclusions/Significance:This is the first reported 3D structure of an Anisakis allergen. Magnesium ion binding and structural resemblance to Calmodulin, suggest some putative functions for SXP/RAL-2 proteins. Furthermore, the IgE/IgG4 binding regions of Ani s 5 were identified as segments localized on its surface. These data will contribute towards a better understanding of the interactions that occur between immunoglobulins and allergens and, in turn, facilitate

Actinoporins are water-soluble proteins with the ability to form pores upon insertion into biological membranes. They constitute a family of proteins with high degree of sequence identities but different hemolytic activities, suggesting that minor conformational arrangements result in major functional changes. A good example of this situation is the sea anemone Stichodactyla helianthus which produces two very similar actinoporins, sticholysins I (StnI) and II (StnII), but of very different hemolytic efficiency. Within this idea, given that the high resolution three-dimensional structure of StnII is already known, we have now solved that one corresponding to StnI in order to analyze the influence of particular residues on the conformation and activity of these proteins. In addition, random mutagenesis has been also used to produce five less hemolytic variants of StnI. All these mutations map to functionally relevant regions because they are probably involved in conformational changes associated with pore formation, which take place after membrane binding, and involve long-distance rearrangements of the polypeptide chain of actinoporins.

Onconase® is a highly cytotoxic amphibian homolog of Ribonuclease A. Here, we describe the construction of circularly permuted Onconase® variants by connecting the N- and C-termini of this enzyme with amino acid residues that are recognized and cleaved by the human immunodeficiency virus protease. Uncleaved circularly permuted Onconase® variants are unusually stable, non-cytotoxic and can internalize in human T-lymphocyte Jurkat cells. The structure, stability and dynamics of an intact and a cleaved circularly permuted Onconase® variant were determined by Nuclear Magnetic Resonance spectroscopy and provide valuable insight into the changes in catalytic efficiency caused by the cleavage. The understanding of the structural environment and the dynamics of the activation process represents a first step toward the development of more effective drugs for the treatment of diseases related to pathogens expressing a specific protease. By taking advantage of the protease's activity to initiate a cytotoxic cascade, this approach is thought to be less susceptible to known resistance mechanisms.

Protein-glycosaminoglycan interactions are essential in many biological processes and human diseases, yet how their recognition occurs is poorly understood. Eosinophil cationic protein (ECP) is a cytotoxic ribonuclease that interacts with glycosaminoglycans at the cell surface; this promotes the destabilization of the cellular membrane and triggers ECP's toxic activity. To understand this membrane destabilization event and the differences in the toxicity of ECP and its homologues, the high resolution solution structure of the complex between full length folded ECP and a heparin-derived trisaccharide (O-iPr-¿-d-GlcNS6S-¿(1-4)-l-IdoA2S-¿(1-4)-d-GlcNS6S) has been solved by NMR methods and molecular dynamics simulations. The bound protein retains the tertiary structure of the free protein. The (2)S(0) conformation of the IdoA ring is preferably recognized by the protein. We have identified the precise location of the heparin binding site, dissected the specific interactions responsible for molecular recognition, and defined the structural requirements for this interaction. The structure reveals the contribution of Arg7, Gln14, and His15 in helix ¿1, Gln40 in strand ß1, His64 in loop 4, and His128 in strand ß6 in the recognition event and corroborates the previously reported participation of residues Arg34-Asn39. The participation of the catalytic triad (His15, Lys38, His128) in recognizing the heparin mimetic reveals, at atomic resolution, the mechanism of heparin's inhibition of ECP's ribonucleolytic activity. We have integrated all the available data to propose a molecular model for the membrane interaction process. The solved NMR complex provides the structural model necessary to design inhibitors to block ECP's toxicity implicated in eosinophil pathologies.

Amyloidogenic neurodegenerative diseases are incurable conditions caused by specific largely disordered proteins. However, the underlying molecular mechanism remains elusive. A favored hypothesis postulates that a critical conformational change in the monomer (an ideal therapeutic target) in these ‘‘neurotoxic proteins’’ triggers the pathogenic cascade. Using force spectroscopy with unequivocal single-molecule identification we demonstrate a rich conformational polymorphism at their monomer level. This polymorphism strongly correlates with amyloidogenesis and neurotoxicity: it is absent in a fibrillization-incompetent mutant, favored by familial-disease mutations and diminished by a surprisingly promiscuous inhibitor of the monomeric b-conformational change and neurodegeneration. The demonstrated ability to inhibit the conformational heterogeneity of these proteins by a single pharmacological agent reveals common features in the monomer and suggests a common pathway to diagnose, prevent, halt or reverse multiple neurodegenerative diseases

Eosinophil Cationic Protein (ECP) is a cytotoxic RNase present in large amounts in the eosinophil granules. During inflammation, it is secreted and plays a role in host defence with bactericidal, antiviral, and antiparasitic activities. Cationic and aromatic residues have been reported to be essential for its interaction with membranes1 and glycosaminoglycans (GAGs)2, suggesting that recognition of heparan sulphates exposed at the mammalian cellular surfaces may drive and modulate its cytotoxicity3. To get deeper insight into the cytotoxic process we have explored the interactions of ECP with a GAG mimetic. By using NMR spectroscopy and MD simulations we have determined the 3D structure of ECP in complex with a representative trisaccharide heparinderivative. We have also estimated its binding affinity (µM range). The complex structure reveals that the carbohydrate binds at the catalytic site and that the charged sulphate and carboxylate groups are clustered with well-defined orientations. Charged and polar residues, and the conserved W10 of ECP are involved in the recognition. The pyranose ring of IdoA adopts the skew-boat 2S0 conformation as observed in other complexes4. This recognition event may constitute the first step of the ECP’s cytotoxic mechanism of action by facilitating contacts with the membrane that would then trigger membrane destabilization and cell death.

Eosinophil Cationic Protein (ECP) is a highly stable cytotoxic RNase of 133 aminoacids present in large amounts in the eosinophil granules. In inflammatory processes, following eosinophil activation the protein is secreted and plays a role in host defence with bactericidal, antiviral, and antiparasitic activities. Remarkably, a large number of Arg residues in the protein surface confers a high cationicity and have been related to ECP’s potent cytotoxicity by facilitating the interaction with membranes. Aromatic residues have also been shown to importantly contribute to this activity. These residues have also been reported to be essential for the interaction with glycosaminoglycans (GAGs), such as heparin, suggesting that recognition of heparan sulphates exposed at the mammalian cellular surfaces may drive and modulate its cytotoxicity. To get deeper insight into the cytotoxic process, here we further our previous work3 and explore the interactions of ECP with a GAG mimetic. By using NMR spectroscopy and molecular dynamic simulations we have determined the solution structure of ECP in complex with a representative trisaccharide heparin-derivative as a good model for the highly sulphated Sdomains of heparan sulphate. We have also estimated its binding affinity (µM range) on the basis of chemical shift perturbation data. Filtered experiments were useful to define the orientation of the carbohydrate in the binding pocket, which was found to occupy the catalytic site. The complex structure reveals that the charged sulphate and carboxylate groups of the carbohydrate are clustered at the binding site with well-defined orientations with respect to the protein favouring electrostatic interactions to be established. Charged and polar residues, as well as the conserved aromatic residue W10 play essential roles in the recognition. Interestingly, the skew-boat 2 S0 conformation for the pyranose ring of IdoA is clearly preferred as observed in other complexes4 . This recognition

Eosinophil Cationic Protein (ECP) is a highly stable cytotoxic RNase of 133 aminoacids present in large amounts in the eosinophil granules. In inflammatory processes, following eosinophil activation the protein is secreted and plays a role in host defence with bactericidal, antiviral, and antiparasitic activities. Remarkably, a large number of Arg residues in the protein surface confers a high cationicity and have been related to ECP’s potent cytotoxicity by facilitating the interaction with membranes. Aromatic residues have also been shown to importantly contribute to this activity. These residues have also been reported to be essential for the interaction with glycosaminoglycans (GAGs), such as heparin, suggesting that recognition of heparan sulphates exposed at the mammalian cellular surfaces may drive and modulate its cytotoxicity. To get deeper insight into the cytotoxic process, here we further our previous work3 and explore the interactions of ECP with a GAG mimetic. By using NMR spectroscopy and molecular dynamic simulations we have determined the solution structure of ECP in complex with a representative trisaccharide heparin-derivative as a good model for the highly sulphated Sdomains of heparan sulphate. We have also estimated its binding affinity (µM range) on the basis of chemical shift perturbation data. Filtered experiments were useful to define the orientation of the carbohydrate in the binding pocket, which was found to occupy the catalytic site. The complex structure reveals that the charged sulphate and carboxylate groups of the carbohydrate are clustered at the binding site with well-defined orientations with respect to the protein favouring electrostatic interactions to be established. Charged and polar residues, as well as the conserved aromatic residue W10 play essential roles in the recognition. Interestingly, the skew-boat 2 S0 conformation for the pyranose ring of IdoA is clearly preferred as observed in other complexes4 . This recognition

Human Tubulin Binding Cofactor C (TBCC) is a two-domain 346-aminoacid protein involved in the post-chapero nin folding pathway of a- and -tubulin monomers. In association with other cofactors, TBCC forms a supercomplex in the ultimate folding steps inducing the GTP hydrolysis that leads to the release of productive tubulin heterodimers ready to polymerize into microtubules. 1.2 We have used NMR spectroscopy to determine the 3D structure of the N-terminal domain of TBCC.3 The domain adopts a spectrin-like fold topology composed of an antiparallel three­ helix bundle connected by short loops. Remarkably, our NMR data reveal that the 30-residue N-terminal fragment of the domain remains flexible and disordered in solution, although several regions retain significant helical propensities. We show that the N-t erminal domain of TBCC interacts with the a -tubulin dimer and that the N-terminal 30-residue fragment actively participates in the binding event.3 This fragment contains a sequence stretch that concentrates positively charged residues, leading to the proposal of a likely electrostatically-driven molecular recognition process involving the acidic hypervariable regions of tubulin monomers

Ribonucleases (RNases) participate in a number of different and crucial biological functions beyond their common “housekeeping” ribonucleolytic activity. Some of them show intrinsic cytotoxicity and play important roles in the innate immune system with bactericidal, antiviral, and antiparasitic activities. Due to their small size and high stability, RNases have been extensively characterised and widely used as models in many biophysical studies. We have long employed NMR to determine the 3D structure, stability, folding, electrostatics, internal dynamics and intermolecular interactions of RNases, and used these data to gain insights into biological activities. Here, I will briefly present our recent NMR results on human RNase 1 (HP-RNase) [1], RNase 3 (ECP) [2,3,4,5], bovine pancreatic RNase A [6,7,8] and Onconase® zymogens [9]. On the bases of these data, the structure-activity relationship for these proteins will be described with special emphasis on the molecular determinants of ECP’s cytotoxic mechanism related to its interaction with membranes. By using NMR spectroscopy and molecular dynamic simulations, we have studied the interaction with micelles and determined the solution structure of ECP in complex with a representative trisaccharide heparin-derivative as a good model for the highly sulphated S-domains of heparan sulphate. We have also estimated its binding affinity (µM range) on the basis of chemical shift perturbation data. The structure of the complex reveals structural insights into the recognition event that may constitute the first step of the ECP’s cytotoxic mechanism of action.

Amyloidogenic neurodegenerative diseases are incurable conditions caused by specific largely disordered proteins. However, the underlying molecular mechanism remains elusive. A favored hypothesis postulates that a critical conformational change in the monomer (an ideal therapeutic target) in these ‘‘neurotoxic proteins’’ triggers the pathogenic cascade. Using force spectroscopy with unequivocal singlemolecule identification we demonstrate a rich conformational polymorphism at their monomer level. This polymorphism strongly correlates with amyloidogenesis and neurotoxicity: it is absent in a fibrillization-incompetent mutant, favored by familial-disease mutations and diminished by a surprisingly promiscuous inhibitor of the monomeric b-conformational change and neurodegeneration. The demonstrated ability to inhibit the conformational heterogeneity of these proteins by a single pharmacological agent reveals common features in the monomer and suggests a common pathway to diagnose, prevent, halt or reverse multiple neurodegenerative diseases

The bacterium Geobacter sulfurreducens (Gs) can grow in the presence of extracellular terminal acceptors, a property that is currently explored to harvest electricity from aquatic sediments and waste organic matter into microbial fuel cells. A family composed of five triheme cytochromes (PpcA-E) was identified in Gs. These cytochromes play a crucial role by bridging the electron transfer from oxidation of cytoplasmic donors to the cell exterior and assisting the reduction of extracellular terminal acceptors. The detailed thermodynamic characterization of such proteins showed that PpcA and PpcD have an important redox-Bohr effect that might implicate these proteins in the e -/H + coupling mechanisms to sustain cellular growth. The physiological relevance of the redox-Bohr effect in these proteins was studied by determining the fractional contribution of each individual redox-microstate at different pH values. For both proteins, oxidation progresses from a particular protonated microstate to a particular deprotonated one, over specific pH ranges. The preferred e -/H + transfer pathway established by the selected microstates indicates that both proteins are functionally designed to couple e -/H + transfer at the physiological pH range for cellular growth.

Gs (Geobacter sulfurreducens) can transfer electrons to the exterior of its cells, a property that makes it a preferential candidate for the development of biotechnological applications. Its genome encodes over 100 cytochromes and, despite their abundance and key functional roles, to date there is no structural information for these proteins in solution. The trihaem cytochrome PpcA might have a crucial role in the conversion of electronic energy into protonmotive force, a fundamental step for ATP synthesis in the presence of extracellular electron acceptors. In the present study, 15N-labelled PpcA was produced and NMR spectroscopy was used to determine its solution structure in the fully reduced state, its backbone dynamics and the pH-dependent conformational changes. The structure obtained is well defined, with an average pairwise rmsd (root mean square deviation) of 0.25 Å (1 Å=0.1 nm) for the backbone atoms and 0.99 Å for all heavy atoms, and constitutes the first solution structure of a Gs cytochrome. The redox-Bohr centre responsible for controlling the electron/proton transfer was identified, as well as the putative interacting regions between PpcA and its redox partners. The solution structure of PpcA will constitute the foundation for studies aimed at mapping out in detail these interacting regions. © The Authors Journal compilation

High molecular weight m-substituted poly(ether ketone-ketone) has been synthesized by electrophilic precipitation polycondensation via two different ways: reaction of isophthaloyl chloride with diphenyl ether and reaction of isophthaloyl chloride with 1,3-bis(4-phenoxybenzoyl)benzene. The second way of synthesis was found to give structurally more perfect polymers with higher molecular weights. In both cases polycondensation proceeded with precipitation of the polymers formed as uniform particles. The influence of reaction conditions has been studied. Monomer concentration and monomer stoichiometric ratio were shown to affect the polymer properties.