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Dames S.A.,TU Munich | Dames S.A.,Helmholtz Center Munich | Dames S.A.,Institute of Structural Biology
Journal of Peptide Science | Year: 2015

The nematocyst walls of Hydra are formed by proteins containing small cysteine-rich domains (CRDs) of ~25 amino acids. The first CRD of nematocyst outer all antigen (NW1) and the C-terminal CRD of minicollagen-1 (Mcol1C) contain six cysteines at identical sequence positions, however adopt different disulfide bonded structures. NW1 shows the disulfide connectivities C2-C14/C6-C19/C10-C18 and Mcol1C C2-C18/C6-C14/C10-C19. To analyze if both show structural preferences in the open, non-disulfide bonded form, which explain the formation of either disulfide connectivity pattern, molecular dynamics (MD) simulations at different temperatures were performed. NW1 maintained in the 100-ns MD simulations at 283 K a rather compact fold that is stabilized by specific hydrogen bonds. The Mcol1C structure fluctuated overall more, however stayed most of the time also rather compact. The analysis of the backbone Φ/ψ angles indicated different turn propensities for NW1 and Mcol1C, which mostly can be explained based on published data about the influence of different amino acid side chains on the local backbone conformation. Whereas a folded precursor mechanism may be considered for NW1, Mcol1C may fold according to the quasi-stochastic folding model involving disulfide bond reshuffling and conformational changes, locking the native disulfide conformations. The study further demonstrates the power of MD simulations to detect local structural preferences in rather dynamic systems such as the open, non-disulfide bonded forms of NW1 and Mcol1C, which complement published information from NMR backbone residual dipolar couplings. Because the backbone structural preferences encoded by the amino acid sequence embedding the cysteines influence which disulfide connectivities are formed, the data are generally interesting for a better understanding of oxidative folding and the design of disulfide stabilized therapeutics. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd. Source

Kuklin A.I.,Joint Institute for Nuclear Research | Rogov A.D.,Joint Institute for Nuclear Research | Gorshkova Y.E.,Joint Institute for Nuclear Research | Utrobin P.K.,Moscow Institute of Physics and Technology | And 7 more authors.
Physics of Particles and Nuclei Letters | Year: 2011

The results of experimental and computer-modeling investigations of neutron spectra and fluxes obtained with cold and thermal moderators at the IBR-2 reactor (Joint Institute for Nuclear Research (JINR), Dubna) are presented. These studies are for the YuMO small-angle neutron scattering (SANS) spectrometer (IBR-2 beamline 4). The neutron spectra have been measured for two methane cold moderators for the standard configuration of the SANS instrument. The data from both moderators under different conditions of their operation are compared. The ratio of experimentally determined neutron fluxes of cold and thermal moderators is shown at different wavelengths. Monte Carlo simulations have been carried out to determine the spectra for cold-methane and thermal moderators. The results of calculations of the ratio of neutron fluxes of cold and thermal moderators at different wavelengths are demonstrated. In addition, the absorption of neutrons in the air gaps on the way from the moderator to the investigated sample is presented. SANS with the protein apoferritin was done with both cold methane and a thermal moderator and the data were compared. The prospects for the use of a cold moderator for a SANS spectrometer at IBR-2 are discussed. The advantages of using the YuMO spectrometer with a thermal moderator with respect to the tested cold moderator are shown. © 2011 Pleiades Publishing, Ltd. Source

Holton S.J.,German Electron Synchrotron | Anandhakrishnan M.,German Electron Synchrotron | Geerlof A.,German Electron Synchrotron | Geerlof A.,Institute of Structural Biology | Wilmanns M.,German Electron Synchrotron
Journal of Structural Biology | Year: 2013

Hydroxyacid dehydrogenases, responsible for the stereospecific conversion of 2-keto acids to 2-hydroxyacids in lactic acid producing bacteria, have a range of biotechnology applications including antibiotic synthesis, flavor development in dairy products and the production of valuable synthons. The genome of Lactobacillus delbrueckii ssp. bulgaricus, a member of the heterogeneous group of lactic acid bacteria, encodes multiple hydroxyacid dehydrogenases whose structural and functional properties remain poorly characterized. Here, we report the apo and coenzyme NAD+ complexed crystal structures of the L. bulgaricus D-isomer specific 2-hydroxyacid dehydrogenase, D2-HDH. Comparison with closely related members of the NAD-dependent dehydrogenase family reveals that whilst the D2-HDH core fold is structurally conserved, the substrate-binding site has a number of non-canonical features that may influence substrate selection and thus dictate the physiological function of the enzyme. © 2012 Elsevier Inc. Source

Sachyani D.,Institute of Structural Biology | Dvir M.,Tel Aviv University | Strulovich R.,Institute of Structural Biology | Tria G.,German Electron Synchrotron | And 7 more authors.
Structure | Year: 2014

Kv7 channels tune neuronal and cardiomyocyte excitability. In addition to the channel membrane domain, they also have a unique intracellular C-terminal (CT) domain, bound constitutively to calmodulin (CaM). This CT domain regulates gating and tetramerization. We investigated the structure of the membrane proximal CT module in complex with CaM by X-ray crystallography. The results show how the CaM intimately hugs a two-helical bundle, explaining many channelopathic mutations. Structure-based mutagenesis of this module in the context of concatemeric tetramer channels and functional analysis along with in vitro data lead us to propose that one CaM binds to one individual protomer, without crosslinking subunits and that this configuration is required for proper channel expression and function. Molecular modeling of the CT/CaM complex in conjunction with small-angle X-ray scattering suggests that the membrane proximal region, having a rigid lever arm, is a critical gating regulator. © 2014 Elsevier Ltd. Source

Scarsdale J.N.,Institute of Structural Biology | Walavalkar N.M.,Virginia Commonwealth University | Buchwald W.A.,Virginia Commonwealth University | Ginder G.D.,University of North Carolina at Chapel Hill | Williams Jr. D.C.,University of North Carolina at Chapel Hill
Journal of Biological Chemistry | Year: 2014

Although highly homologous to other methylcytosine-binding domain (MBD) proteins, MBD3 does not selectively bind methylated DNA, and thus the functional role of MBD3 remains in question. To explore the structural basis of its binding properties and potential function, we characterized the solution structure and binding distribution of the MBD3 MBD on hydroxymethylated, methylated, and unmethylated DNA. The overall fold of this domain is very similar to other MBDs, yet a key loop involved in DNA binding is more disordered than previously observed. Specific recognition of methylated DNA constrains the structure of this loop and results in large chemical shift changes in NMR spectra. Based on these spectral changes, we show that MBD3 preferentially localizes to methylated and, to a lesser degree, unmethylated cytosine-guanosine dinucleotides (CpGs), yet does not distinguish between hydroxymethylated and unmethylated sites. Measuring residual dipolar couplings for the different bound states clearly shows that the MBD3 structure does not change between methylation-specific and nonspecific binding modes. Furthermore, residual dipolar couplings measured for MBD3 bound to methylated DNA can be described by a linear combination of those for the methylation and nonspecific binding modes, confirming the preferential localization to methylated sites. The highly homologous MBD2 protein shows similar but much stronger localization to methylated as well as unmethylated CpGs. Together, these data establish the structural basis for the relative distribution of MBD2 and MBD3 on genomic DNA and their observed occupancy at active and inactive CpG-rich promoters. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc. Source

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