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Voltage-gated ion channels, whose first identified function was to generate action potentials, are divided into subfamilies with numerous members. The family of voltage-gated proton channels (HV) is tiny. To date, all species found to express HV have exclusively one gene that codes for this unique ion channel. Here we report the discovery and characterization of three proton channel genes in the classical model system of neural plasticity, Aplysia californica. The three channels (AcHV1, AcHV2, and AcHV3) are distributed throughout the whole animal. Patch-clamp analysis confirmed proton selectivity of these channels but they all differed markedly in gating. AcHV1 gating resembled HV in mammalian cells where it is responsible for proton extrusion and charge compensation. AcHV2 activates more negatively and conducts extensive inward proton current, properties likely to acidify the cytosol. AcHV3, which differs from AcHV1 and AcHV2 in lacking the first arginine in the S4 helix, exhibits proton selective leak currents and weak voltage dependence. We report the expansion of the proton channel family, demonstrating for the first time the expression of three functionally distinct proton channels in a single species.

(Δ)pH induces conformational change from a deactivated to an activated state of the hHv1 voltage-gated proton channel.

Voltage-gated proton channels (HV1) are essential for various physiological tasks but are strongly inhibited by Zn2+ cations. Some determinants of Zn2+ binding have been elucidated experimentally and in computational studies. However, the results have always been interpreted under the assumption that Zn2+ binds to monomeric HV1 despite evidence that HV1 expresses as a dimer and that the dimer has a higher affinity for zinc than the monomer and experimental data that suggest coordination in the dimer interface. The results of former studies are also controversial, e.g., supporting either one single or two binding sites. Some structural determinants of the binding are still elusive. We performed a series of molecular dynamics simulations to address different structures of the human proton channel, the monomer and two plausible dimer conformations, to compare their respective potential to interact with and bind Zn2+ via the essential histidines. The series consisted of several copies of the system to generate independent trajectories and increase the significance compared to a single simulation. The amount of time simulated totals 29.9 μs for 126 simulations of systems comprising ∼59,000 to ∼187,000 atoms. Our approach confirms the existence of two binding sites in monomeric and dimeric human HV1. The dimer interface is more efficient for attracting and binding Zn2+ via the essential histidines than the monomer or a dimer with the histidines in the periphery. The higher affinity is due to the residues in the dimer interface that create an attractive electrostatic potential funneling the zinc cations toward the binding sites.

Voltage-gated proton channels (H(V)1) are essential for various physiological tasks but are strongly inhibited by Zn(2+) cations. Some determinants of Zn(2+) binding have been elucidated experimentally and in computational studies. However, the results have always been interpreted under the assumption that Zn(2+) binds to monomeric H(V)1 despite evidence that H(V)1 expresses as a dimer and that the dimer has a higher affinity for zinc than the monomer and experimental data that suggest coordination in the dimer interface. The results of former studies are also controversial, e.g., supporting either one single or two binding sites. Some structural determinants of the binding are still elusive. We performed a series of molecular dynamics simulations to address different structures of the human proton channel, the monomer and two plausible dimer conformations, to compare their respective potential to interact with and bind Zn(2+) via the essential histidines. The series consisted of several copies of the system to generate independent trajectories and increase the significance compared to a single simulation. The amount of time simulated totals 29.9 μs for 126 simulations of systems comprising ∼59,000 to ∼187,000 atoms. Our approach confirms the existence of two binding sites in monomeric and dimeric human H(V)1. The dimer interface is more efficient for attracting and binding Zn(2+) via the essential histidines than the monomer or a dimer with the histidines in the periphery. The higher affinity is due to the residues in the dimer interface that create an attractive electrostatic potential funneling the zinc cations toward the binding sites.

The interaction of proteins with other biomolecules plays a central role in various aspects of the structural and functional organization of the cell. Their elucidation is crucial to understand processes such as metabolic control, signal transduction, and gene regulation. However, an experimental structural characterization of all of them is impractical, and only a small fraction of the potential complexes will be amenable to direct experimental analysis. Docking represents a versatile and powerful method to predict the geometry of protein–protein complexes. However, despite significant methodical advances, the identification of good docking solutions among a large number of false solutions still remains a difficult task. The present work allowed to adapt the formalism of mutual information (MI) from information theory to protein docking. In this context, we have developed a method, which finds a lower bound for the MI between a binary and an arbitrary finite random variable with joint distributions that have a variational distance not greater than a known value to a known joint distribution. This lower bound can be applied to MI estimation with confidence intervals. Different from previous results, these confidence intervals do not need any assumptions on the distribution or the sample size. An MI-based optimization protocol in conjunction with a clustering procedure was used to define reduced amino acids alphabets describing the interface properties of protein complexes. The reduced alphabets were subsequently converted into a scoring function for the evaluation of docking solutions, which is available for public use via a web service. The approach outlined above has recently been extended to the analysis of protein–DNA complexes by taking also into account geometrical parameters of the DNA.

Author(s): Fechner, Uli; de Graaf, Chris; Torda, Andrew E; Gussregen, Stefan; Evers, Andreas; Matter, Hans; Hessler, Gerhard; Richmond, Nicola J; Schmidtke, Peter; Segler, Marwin HS; Waller, Mark P; Pleik, Stefanie; Shea, Joan-Emma; Levine, Zachary; Mullen, Ryan; van den Broek, Karina; Epple, Matthias; Kuhn, Hubert; Truszkowski, Andreas; Zielesny, Achim; Fraaije, Johannes Hans; Gracia, Ruben Serral; Kast, Stefan M; Bulusu, Krishna C; Bender, Andreas; Yosipof, Abraham; Nahum, Oren; Senderowitz, Hanoch; Krotzky, Timo; Schulz, Robert; Wolber, Gerhard; Bietz, Stefan; Rarey, Matthias; Zimmermann, Markus O; Lange, Andreas; Ruff, Manuel; Heidrich, Johannes; Onlia, Ionut; Exner, Thomas E; Boeckler, Frank M; Bermudez, Marcel; Firaha, Dzmitry S; Holloczki, Oldamur; Kirchner, Barbara; Tautermann, Christofer S; Volkamer, Andrea; Eid, Sameh; Turk, Samo; Rippmann, Friedrich; Fulle, Simone; Saleh, Noureldin; Saladino, Giorgio; Gervasio, Francesco L; Haensele, Elke; Banting, Lee; Whitley, David C; Oliveira Santos, Jana Sopkova-de; Bureau, Ronan; Clark, Timothy; Sandmann, Achim; Lanig, Harald; Kibies, Patrick; Heil, Jochen; Hoffgaard, Franziska; Frach, Roland; Engel, Julian; Smith, Steven; Basu, Debjit; Rauh, Daniel; Kohlbacher, Oliver; Boeckler, Frank M; Essex, Jonathan W; Bodnarchuk, Michael S; Ross, Gregory A; Finkelmann, Arndt R; Goller, Andreas H; Schneider, Gisbert; Husch, Tamara; Schutter, Christoph; Balducci, Andrea; Korth, Martin; Ntie-Kang, Fidele; Gunther, Stefan; Sippl, Wolfgang; Mbaze, Luc Meva'a

Inactivation of signal transducers and activators of transcription (STAT) proteins is regulated by dual-specificity phosphatases (DSPs) with high substrate specificity. Although experiments have provided useful information about the phosphatase activity and the specificity for STATs, there is up-to-date no data at a molecular level to explain the specific recognition of STAT substrates by this subfamily of phosphatases. Here, a combined approach of molecular modeling, docking and molecular dynamics simulations was used to address the binding between DSPs and their STAT substrates. We identified a binding interface at the protein tyrosine phosphatase (PTP) domain of the DSP VHR that interacts with the SH2-domain of STAT5. This finding is consistent with previous mutational data and supports a "two-step" mechanism for the dephosphorylation event. Application of the same approach suggests the presence of a similar interface between the viral DSP VH1 and STAT1. Furthermore, the interaction network at this interface provides an explanation for the specificity of the DSP-STAT recognition.

In molecular communication (MC) systems, the expected number of molecules observed at the receiver over time after the instantaneous release of molecules by the transmitter is referred to as the channel impulse response (CIR). Knowledge of the CIR is needed for the design of detection and equalization schemes. In this paper, we present a training-based CIR estimation framework for MC systems which aims at estimating the CIR based on the observed number of molecules at the receiver due to emission of a sequence of known numbers of molecules by the transmitter. In particular, we derive maximum likelihood (ML) and least sum of square errors (LSSE) estimators. We also study the Cramer Rao (CR) lower bound and training sequence design for the considered system. Simulation results confirm the analysis and compare the performance of the proposed estimation techniques with the CR lower bound., This paper has been submitted for presentation at IEEE International Conference on Communications (ICC) 2016

Electronic structures of the ternary metal borocarbide compounds Sc2BC2, Al3BC3 and Lu3BC3 containing linear BC2 units are compared using density functional calculations. Results reveal a covalent bonding between the metallic matrix and the formally BC25− nonmetal anions which is stronger for the aluminum compound than for the two others.

Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

In this paper a numerical method is presented, which finds a tight lower bound for the mutual information between a binary and an arbitrary finite random variable with joint distributions that have variational distance to a known joint distribution not greater than a known value. This lower bound can be applied to mutual information estimation with confidence intervals.

The synthesis by arc-melting techniques, the single-crystal X-ray structure, and the theoretical analysis of Gd4B3C4 are reported. It crystallizes in the triclinic space group P1 with a = 3.637(2) A, b = 3.674(2) A, c = 11.859(5) A, alpha = 93.34(5) degrees, beta = 96.77(5) degrees, gamma = 90.24(5) degrees, and Z = 1. In this structure, the boron and carbon atoms form two different types of nonmetal arrangements: 1-D (BC)infinity branched chains and finite (0-D) linear CBC "molecular" units. Gd4B3C4 is the first characterized member of the rare earth metal borocarbide series in which both 1-D and "molecular" 0-D nonmetal atom systems coexist. From the structural and theoretical analysis, the following formal charge distribution can be proposed within the ionic limit: (Gd3+)4(BC2(5-)(BC3-)2.e-. Tight-binding calculations suggest that the excess electron in the ionic limit is mainly localized on the Gd atoms (at the bottom of the 5d band), while LAPW calculations favor its localization on the (BC)infinity chain. The bonding within this compound is fully analyzed and compared to other members of the rare earth metal borocarbide series.

The borocarbides R 5 B 2 C 5 ( R =Y, Ce–Tm) were prepared by arc melting from the pure rare-earth metals, boron and carbon. The structural arrangement of these compounds, which crystallize in the tetragonal space group P 4/ ncc , consists of a three-dimensional framework of rare-earth atoms resulting from the stacking of slightly corrugated two-dimensional squares, which lead to the formation of octahedral holes and distorted bicapped square antiprismatic cavities filled with isolated carbon atoms and C–B–C chains, respectively. In contrast to the heavy rare-earth metal (Gd–Tm)-containing compounds which melt congruently, those with the early rare-earth elements (Ce–Sm) are formed peritectically. The electronic structure and chemical bonding of Sm 5 B 2 C 5 and Gd 5 B 2 C 5 are analyzed using extended Huckel tight-binding and density-functional theory calculations. Results reveal a rather strong covalency between the metallic matrix and the BC 2 groups and the isolated carbon atoms, respectively, similar to what is generally computed in related rare-earth metal borocarbides. Magnetic susceptibility measurements indicate that all samples, which were investigated, undergo ferromagnetic transitions in the temperature region below T =130 K. The heavy rare-earth metal (Tb–Tm) borocarbides exhibit a magnetic behavior typical of narrow-domain-wall ferromagnets. Both the Curie temperatures, T C , as well as the paramagnetic Curie temperatures, Θ P , scale approximately with the de Gennes factor. Hence the indirect exchange interaction via conduction electrons (RKKY-interacting) is the dominating force of the R – R coupling mechanism.

Three-coordinate boron, isoelectronic with a trigonal planar carbonium ion, possesses a vacant p orbital which can conjugate with an organic π system and thus serve as a π acceptor. We and others have prepared a series of symmetric compounds of the general form (mes)2 B⇐X⇒B(mes)2 [mes=mesityl=2,4,6 Me3C6H2; ⇐X⇒=conjugated organic π system such as –(p-C6H4)n– or trans–trans–CH=CH–(p-C6H4)n–CH=CH–] as well as donor–acceptor compounds of the general form D⇒X⇒B(mes)2 [D=π donor such as MeO, MeS, H2N, Me2N, Ph2P, ferrocenyl; ⇒X⇒=conjugated organic π system such as –C6H4–, –C6H4–CH=CH–, –C6H4–C≡C–, –C6H4–CH=CH–C6H4–] and examined representative single-crystal structures as well as linear (UV–vis absorption and fluorescence) and second- and third-order nonlinear optical properties (by electric field-induced second harmonic generation (EFISH) and third harmonic generation (THG)). The bulky mesityl groups protect the boron centers from hydrolysis. Many of the compounds are highly fluorescent, with the unsymmetric ones displaying limited solvatochromic behavior in absorption spectra but significant solvatochromic effects in their emission spectra consistent with small dipole moments in the ground state and large dipole moments in the excited states. Results from other groups on the use of related boron compounds as either electron-transport materials or emitting agents in electroluminescent devices, and on the preparation and optical properties of three-coordinate boron-containing conjugated polymers are presented. Preliminary results of extended Huckel (EH) and density functional (DF) molecular-orbital calculations on representative symmetric diboron compounds and extended Huckel tight-binding (EHTB) calculations on a model boron-containing polymer are reported. The B(mes)2 group is a good π acceptor, and three-coordinate boron moieties show significant promise for use in molecular and polymeric optical materials.

By combining a bound on the absolute value of the difference of mutual information between two joint probablity distributions with a fixed variational distance, and a bound on the probability of a maximal deviation in variational distance between a true joint probability distribution and an empirical joint probability distribution, confidence intervals for the mutual information of two random variables with finite alphabets are established. Different from previous results, these intervals do not need any assumptions on the distribution and the sample size., 5 pages, 2 figure

The multifunctional protein kinase pUL97 of human cytomegalovirus (HCMV) strongly determines the efficiency of virus replication. Previously, the existence of two pUL97 isoforms that arise from alternative translational initiation and show a predominant nuclear localization was described. Two bipartite nuclear localization sequences, NLS1 and NLS2, were identified in the N terminus of the large isoform, whilst the small isoform exclusively contained NLS2. The current study found the following: (i) pUL97 nuclear localization in HCMV-infected primary fibroblasts showed accumulations in virus replication centres and other nuclear sections; (ii) in a quantitative evaluation system for NLS activity, the large isoform showed higher efficiency of nuclear translocation than the small isoform; (iii) NLS1 was mapped to aa 6–35 and NLS2 to aa 190–213; (iv) using surface plasmon resonance spectroscopy, the binding of both NLS1 and NLS2 to human importin-α was demonstrated, stressing the importance of individual arginine residues in the bipartite consensus motifs; (v) nuclear magnetic resonance spectroscopy of pUL97 peptides confirmed an earlier statement about the functional requirement of NLS1 embedding into an intact α-helical structure; and (vi) a bioinformatics investigation of the solvent-accessible surface suggested a high accessibility of NLS1 and an isoform-specific, variable accessibility of NLS2 for interaction with importin-α. Thus, the nucleocytoplasmic transport mechanism of the isoforms appeared to be differentially regulated, and this may have consequences for isoform-dependent functions of pUL97 during virus replication.

Constitutive STAT signaling provides growth promoting signals in many forms of malignancy. We performed molecular modeling and molecular dynamics studies of the interaction between the regulatory Src homology 2 (SH2) domains of STAT3 and 6 with phosphorylated peptides of the herpesviral oncoprotein Tip, which facilitates Src kinase mediated STAT-activation and T cell proliferation. The studies give insight into the ligand binding specificity of the STAT SH2 domains and provide the first model for the differential activation of STAT3 or STAT6 by two distinct regions of the viral Tip protein. The biological relevance of the modeled interactions was then confirmed by activation studies using corresponding recombinant oncoproteins, and finally by respective recombinant viruses. The functional data give experimental validation of the molecular dynamics study, and provide evidence for the involvement of STAT6 in the herpesvirus induced T cell proliferation.

The pUL97 protein kinase encoded by human cytomegalovirus is a multifunctional determinant of the efficiency of viral replication and phosphorylates viral as well as cellular substrate proteins. Here, we report that pUL97 is expressed in two isoforms with molecular masses of approximately 90 and 100 kDa. ORF UL97 comprises an unusual coding strategy in that five in-frame ATG start codons are contained within the N-terminal 157 aa. Site-directed mutagenesis, transient expression of point and deletion mutants and proteomic analyses accumulated evidence that the formation of the large and small isoforms result from alternative initiation of translation, with the start points being at amino acids 1 and 74, respectively. In vitro kinase assays demonstrated that catalytic activity, in terms of autophosphorylation and histone substrate phosphorylation, was indistinguishable for the two isoforms. An analysis of the intracellular distribution of pUL97 by confocal laser-scanning microscopy demonstrated that both isoforms have a pronounced nuclear localization. Surprisingly, mapping experiments performed to identify the nuclear localization signal (NLS) of pUL97 strongly suggest that the mechanism of nuclear transport is distinct for the two isoforms. While the extreme N terminus (large isoform) comprises a highly efficient, bipartite NLS (amino acids 6-35), a second sequence apparently conferring a less efficient mode of nuclear translocation was identified downstream of amino acid 74 (small and large isoforms). Taken together, the findings argue for a complex mechanism of nuclear translocation for pUL97 which might be linked with fine-regulatory differences between the two isoforms.

Background The TetR family member AmtR is the central regulator of nitrogen starvation response in Corynebacterium glutamicum. While the AmtR regulon was physiologically characterized in great detail up to now, mechanistic questions of AmtR binding were not addressed. This study presents a characterization of functionally important amino acids in the DNA binding domain of AmtR and of crucial nucleotides in the AmtR recognition motif. Results Site-directed mutagenesis, the characterization of corresponding mutant proteins by gel retardation assays and surface plasmon resonance and molecular modelling revealed several amino acids, which are directly involved in DNA binding, while others have more structural function. Furthermore, we could show that the spacing of the binding motif half sites is crucial for repression of transcription by AmtR. Conclusion Although the DNA binding domain of TetR-type repressors is highly conserved and a core binding motif was identified for AmtR and TetR(D), the AmtR binding domain shows individual properties compared to other TetR proteins. Besides by distinct amino acids of AmtR, DNA binding is influenced by nucleotides not only of the conserved binding motif but also by spacing nucleotides in C. glutamicum.

Phosphoryl transfer is a key reaction in many aspects of metabolism, gene regulation, and signal transduction. One prominent example is the phosphoenolpyruvate:sugar phosphotransferase system (PTS), which represents an integral part of the bacterial sugar metabolism. The transfer between the enzymes IIA (Glc) and IIB (Glc) in the glucose-specific branch of the PTS is of particular interest due to the unusual combination of donor and acceptor residues involved in phosphoryl transfer: The phosphoryl group is initially attached to the Nepsilon2 atom of His 90 in IIA (Glc) and then transferred to the S gamma atom of Cys 35 in IIB (Glc). To gain insight into the details of the transfer mechanism, we have performed a QM/MM simulation which treats the entire active site quantum-mechanically. The transfer has a high dissociative character, and the Nepsilon2-P bond gets immediately destabilized after complex formation by numerous interactions formed between residues of IIB (Glc) and the phosphoryl group. The final formation of a tight S gamma-P bond is accompanied by a reorientation of the side chain of the phosphoryl donor. This reorientation results in the loss of interaction between the imidazole ring and the phosphate group thus hindering the reverse transfer. A comparison to the transfer in protein tyrosine phosphatases, which also use a cysteine as acceptor of the phosphoryl group, reveals significant similarities in the conformation of the active site, the energy profile of the reaction, and in the pattern of interactions that stabilize the phosphoryl group during the transfer.

International audience; The (p-R-phenyl)dimesitylboranes (R=Me(2)N, MeO, MeS, Br, I), (p-R-phenylethynyl)dimesitylboranes (R=Me(2)N, MeO, MeS, H), (E)-[2-(p-R-phenyl)ethenyl]dimesitylboranes (R=Me(2)N, H(2)N, MeO, MeS, H, CN, NO(2)), (E)-[2-(2-thienyl)ethenyl]dimesitylborane, and (E)-[2-(o-carboranyl)ethenyl]dimesitylborane have been prepared through the reaction of the appropriate p-R-phenyl- and p-R-phenylethynyllithium reagents with dimesitylboron fluoride and by hydroboration of the appropriate p-R-phenylacetylene, 2-ethynylthiophene, and o-ethynylcarborane with dimesitylborane. Their UV/Vis absorption and emission spectra have been recorded in a range of solvents with the fluorescence maxima of the donor-substituted compounds in particular exhibiting large bathochromic shifts in highly polar solvents, indicative of charge transfer leading to large dipole moments in the excited state. The molecular structures of the (p-R-phenyl)dimesitylboranes (R=Me(2)N, MeO, MeS, Br, I), the (E)-[2-(p-R-phenyl)ethenyl]dimesitylboranes (R=Me(2)N, H(2)N MeO, MeS, H), (p-R-phenylethynyl)dimesitylborane (R=Me(2)N), and (E)-[2-(2-thienyl)ethenyl]dimesitylborane, which have been determined from single-crystal X-ray diffraction measurements, offer evidence of increased conjugation in the ground state with increased donor strength of the R substituent. Their first- and second-order molecular hyperpolarizabilities have been obtained from EFISH and THG measurements, the first-order hyperpolarizabilities being largest for the strongest R-substituent donors. AM1 calculations have been performed on these compounds, showing reasonable agreement with the experimentally obtained bond lengths and hyperpolarizabilities, as well as on several related hypothetical compounds containing multiple C==C bonds, most of which are proposed to have even larger hyperpolarizabilities.

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The synthesis by arc-melting techniques, the single-crystal X-ray structure, and the theoretical analysis of Gd4B3C4 are reported. It crystallizes in the triclinic space group P1 with a = 3.637(2) A, b = 3.674(2) A, c = 11.859(5) A, α = 93.34(5)°, β = 96.77(5)°, γ = 90.24(5)°, and Z = 1. In this structure, the boron and carbon atoms form two different types of nonmetal arrangements: 1-D (BC)∞ branched chains and finite (0-D) linear CBC “molecular” units. Gd4B3C4 is the first characterized member of the rare earth metal borocarbide series in which both 1-D and “molecular” 0-D nonmetal atom systems coexist. From the structural and theoretical analysis, the following formal charge distribution can be proposed within the ionic limit: (Gd3+)4(BC25-)(BC3-)2.e-. Tight-binding calculations suggest that the excess electron in the ionic limit is mainly localized on the Gd atoms (at the bottom of the 5d band), while LAPW calculations favor its localization on the (BC)∞ chain. The bonding within this compound is f...