Kooperativer Bibliotheksverbund

Berlin Brandenburg

and
and

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
Language
Year
  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 27 May 2014, Vol.111(21), pp.7659-64
    Description: The lariat-capping (LC) ribozyme is a natural ribozyme isolated from eukaryotic microorganisms. Despite apparent structural similarity to group I introns, the LC ribozyme catalyzes cleavage by a 2',5' branching reaction, leaving the 3' product with a 3-nt lariat cap that functionally substitutes for a conventional mRNA cap in the downstream pre-mRNA encoding a homing endonuclease. We describe the crystal structures of the precleavage and postcleavage LC ribozymes, which suggest that structural features inherited from group I ribozymes have undergone speciation due to profound changes in molecular selection pressure, ultimately giving rise to an original branching ribozyme family. The structures elucidate the role of key elements that regulate the activity of the LC ribozyme by conformational switching and suggest a mechanism by which the signal for branching is transmitted to the catalytic core. The structures also show how conserved interactions twist residues, forming the lariat to join chemical groups involved in branching.
    Keywords: Gir1 ; RNA Catalysis ; RNA Structure ; Saxs ; Crystallography ; Evolution, Molecular ; Models, Molecular ; Introns -- Genetics ; RNA, Catalytic -- Chemistry ; Signal Transduction -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 2
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 24 September 2013, Vol.110(39), pp.15656-61
    Description: Translation initiation factor 2 (IF2) promotes 30S initiation complex (IC) formation and 50S subunit joining, which produces the 70S IC. The architecture of full-length IF2, determined by small angle X-ray diffraction and cryo electron microscopy, reveals a more extended conformation of IF2 in solution and on the ribosome than in the crystal. The N-terminal domain is only partially visible in the 30S IC, but in the 70S IC, it stabilizes interactions between IF2 and the L7/L12 stalk of the 50S, and on its deletion, proper N-formyl-methionyl(fMet)-tRNA(fMet) positioning and efficient transpeptidation are affected. Accordingly, fast kinetics and single-molecule fluorescence data indicate that the N terminus promotes 70S IC formation by stabilizing the productive sampling of the 50S subunit during 30S IC joining. Together, our data highlight the dynamics of IF2-dependent ribosomal subunit joining and the role played by the N terminus of IF2 in this process.
    Keywords: Integrated Structural Biology ; Protein Synthesis ; Prokaryotic Initiation Factor-2 -- Chemistry ; Ribosome Subunits -- Metabolism ; Thermus Thermophilus -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 3
    Language: English
    In: Langmuir : the ACS journal of surfaces and colloids, 20 August 2013, Vol.29(33), pp.10475-82
    Description: Our studies focused on the determination of aggregation mechanisms of proteins occurring in wine at room temperature. Even if the wine pH range is narrow (2.8 to 3.7), some proteins are affected by this parameter. At low pH, the formation of aggregates and the development of a haze due to proteins sometimes occur. The objective of this work was to determine if the pH impacted the conformational stability of wine proteins. Different techniques were used: circular dichroism and fluorescence spectroscopy to investigate the modification of their secondary and tertiary structure and also SAXS to determine their global shape. Four pure proteins were used, two considered to be stable (invertase and thaumatin-like proteins) and two considered to be unstable (two chitinase isoforms). Two pH values were tested to emphasize their behavior (pH 2.5 and 4.0). The present work highlighted the fact that the conformational stability of some wine proteins (chitinases) was impacted by partial modifications, related to the exposure of some hydrophobic sites. These modifications were enough to destabilize the native state of the protein. These modifications were not observed on wine proteins determined to be stable (invertase and thaumatin-like proteins).
    Keywords: Proteins -- Chemistry ; Wine -- Analysis
    ISSN: 07437463
    E-ISSN: 1520-5827
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 4
    Language: English
    In: Journal of the American Chemical Society, 30 March 2016, Vol.138(12), pp.4155-67
    Description: Modular polyketide synthases (PKSs) direct the biosynthesis of clinically valuable secondary metabolites in bacteria. The fidelity of chain growth depends on specific recognition between successive subunits in each assembly line: interactions mediated by C- and N-terminal "docking domains" (DDs). We have identified a new family of DDs in trans-acyl transferase PKSs, exemplified by a matched pair from the virginiamycin (Vir) system. In the absence of C-terminal partner (VirA (C)DD) or a downstream catalytic domain, the N-terminal DD (VirFG (N)DD) exhibits multiple characteristics of an intrinsically disordered protein. Fusion of the two docking domains results in a stable fold for VirFG (N)DD and an overall protein-protein complex of unique topology whose structure we support by site-directed mutagenesis. Furthermore, using small-angle X-ray scattering (SAXS), the positions of the flanking acyl carrier protein and ketosynthase domains have been identified, allowing modeling of the complete intersubunit interface.
    Keywords: Acyltransferases -- Metabolism ; Polyketide Synthases -- Metabolism ; Virginiamycin -- Chemistry
    ISSN: 00027863
    E-ISSN: 1520-5126
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 5
    Language: English
    In: Journal of bacteriology, 15 February 2015, Vol.197(4), pp.688-98
    Description: Many bacterial pathogens use type three secretion systems (T3SS) to inject virulence factors, named effectors, directly into the cytoplasm of target eukaryotic cells. Most of the T3SS components are conserved among plant and animal pathogens, suggesting a common mechanism of recognition and secretion of effectors. However, no common motif has yet been identified for effectors allowing T3SS recognition. In this work, we performed a biochemical and structural characterization of the Salmonella SopB/SigE chaperone/effector complex by small-angle X-ray scattering (SAXS). Our results showed that the SopB/SigE complex is assembled in dynamic homohexameric-ring-shaped structures with an internal tunnel. In this ring, the chaperone maintains a disordered N-terminal end of SopB molecules, in a good position to be reached and processed by the T3SS. This ring dimensionally fits the ring-organized molecules of the injectisome, including ATPase hexameric rings; this organization suggests that this structural feature is important for ATPase recognition by T3SS. Our work constitutes the first evidence of the oligomerization of an effector, analogous to the organization of the secretion machinery, obtained in solution. As effectors share neither sequence nor structural identity, the quaternary oligomeric structure could constitute a strategy evolved to promote the specificity and efficiency of T3SS recognition.
    Keywords: Bacterial Proteins -- Chemistry ; Molecular Chaperones -- Chemistry ; Salmonella Typhimurium -- Metabolism ; Sigma Factor -- Chemistry
    ISSN: 00219193
    E-ISSN: 1098-5530
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 6
    Language: English
    In: The Journal of biological chemistry, 25 August 2017, Vol.292(34), pp.13904-13913
    Description: RNase P is a universal enzyme that removes 5' leader sequences from tRNA precursors. The enzyme is therefore essential for maturation of functional tRNAs and mRNA translation. RNase P represents a unique example of an enzyme that can occur either as ribonucleoprotein or as protein alone. The latter form of the enzyme, called protein-only RNase P (PRORP), is widespread in eukaryotes in which it can provide organellar or nuclear RNase P activities. Here, we have focused on nuclear PRORP2 and its interaction with tRNA substrates. Affinity measurements helped assess the respective importance of individual pentatricopeptide repeat motifs in PRORP2 for RNA binding. We characterized the PRORP2 structure by X-ray crystallography and by small-angle X-ray scattering in solution as well as that of its complex with a tRNA precursor by small-angle X-ray scattering. Of note, our study reports the first structural data of a PRORP-tRNA complex. Combined with complementary biochemical and biophysical analyses, our structural data suggest that PRORP2 undergoes conformational changes to accommodate its substrate. In particular, the catalytic domain and the RNA-binding domain can move around a central hinge. Altogether, this work provides a refined model of the PRORP-tRNA complex that illustrates how protein-only RNase P enzymes specifically bind tRNA and highlights the contribution of protein dynamics to achieve this specific interaction.
    Keywords: Prorp ; RNA Processing ; X-Ray Crystallography ; Pentatricopeptide Repeat (Ppr) ; Precursor Trna (Pre-Trna) ; Ribonuclease P (Rnase P) ; Small-Angle X-Ray Scattering (Saxs) ; Trna Maturation ; Models, Molecular ; RNA Processing, Post-Transcriptional ; Arabidopsis -- Metabolism ; Arabidopsis Proteins -- Metabolism ; RNA Precursors -- Metabolism ; RNA, Plant -- Metabolism ; RNA, Transfer, Cys -- Metabolism ; Ribonuclease P -- Metabolism
    ISSN: 00219258
    E-ISSN: 1083-351X
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 7
    Language: English
    In: Biomacromolecules, 2013, Vol.14(1), pp.232-239
    Description: Amylose, a linear polymer of alpha(1,4)-linked glucosyl units and a major constituent of starch granules, can also be enzymatically synthesized in vitro from sucrose by bacterial amylosucrases. Depending on the initial sucrose concentration...
    Keywords: Chemical Sciences ; Polymers ; Chemistry
    ISSN: 1525-7797
    E-ISSN: 1526-4602
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 8
    Language: English
    In: Biomacromolecules, 12 March 2018, Vol.19(3), pp.838-848
    Description: The behavior upon immersion in water of two types of starchy materials of biomedical relevance, amorphous potato starch and glycerol-plasticized potato starch, is analyzed in depth. Synchrotron X-ray scattering, specifically wide-angle X-ray scattering (WAXS), and magnetic resonance microimaging (MRμI) are used as very precise and nondestructive quantitative methods to monitor water transfers and structure changes in the samples, with refined spatial and kinetics results. The ingress of water in the cylinder-shaped samples can be inferred from both techniques, and from this, a diffusion mechanism is deduced for each sample type. Qualitatively, scattering and imaging give comparable results: plasticized samples are shown to behave close to a Fickian diffusion case, amorphous samples close to a case II. WAXS results also provide an in-depth knowledge of the crystalline structures associated to each step of the water ingress, and these are in turn correlated to water diffusion. To refine these observations, a recrystallized starch sample is also analyzed via WAXS. This study gives better insight into the structure of a material with a huge biomedical potential (as implants, for example), and for such applications, the behavior upon immersion in water is particularly relevant.
    Keywords: Solanum Tuberosum -- Chemistry ; Starch -- Chemistry ; Water -- Chemistry
    ISSN: 15257797
    E-ISSN: 1526-4602
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 9
    Language: English
    In: Plos One, 8, 2013
    Description: Background: PGC-1 alpha is a crucial regulator of cellular metabolism and energy homeostasis that functionally acts together with the estrogen-related receptors (ERR alpha and ERR gamma) in the regulation of mitochondrial and metabolic gene networks. Dimerization of the ERRs is a pre-requisite for interactions with PGC-1 alpha and other coactivators, eventually leading to transactivation. It was suggested recently (Devarakonda et al) that PGC-1 alpha binds in a strikingly different manner to ERR gamma ligand-binding domains (LBDs) compared to its mode of binding to ERR alpha and other nuclear receptors (NRs), where it interacts directly with the two ERR gamma homodimer subunits. [br/]Methods/Principal Findings: Here, we show that PGC-1 alpha receptor interacting domain (RID) binds in an almost identical manner to ERR alpha and ERR gamma homodimers. Microscale thermophoresis demonstrated that the interactions between PGC-1 alpha RID and ERR LBDs involve a single receptor subunit through high-affinity, ERR-specific L3 and low-affinity L2 interactions. NMR studies further defined the limits of PGC-1 alpha RID that interacts with ERRs. Consistent with these findings, the solution structures of PGC-1 alpha/ERRa LBDs and PGC-1 alpha/ERRc LBDs complexes share an identical architecture with an asymmetric binding of PGC-1 alpha to homodimeric ERR. [br/]Conclusions/Significance: These studies provide the molecular determinants for the specificity of interactions between PGC-1 alpha and the ERRs, whereby negative cooperativity prevails in the binding of the coactivators to these receptors. Our work indicates that allosteric regulation may be a general mechanism controlling the binding of the coactivators to homodimers.
    Keywords: Estrogens – Physiological Aspects ; Estrogens – Comparative Analysis;
    ISSN: 19326203
    E-ISSN: 19326203
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 10
    Language: English
    In: Nucleic acids research, 09 March 2016
    Description: Non-homologous end joining is a ligation process repairing DNA double strand breaks in eukaryotes and many prokaryotes. The ring structured eukaryotic Ku binds DNA ends and recruits other factors which can access DNA ends through the threading of Ku inward the DNA, making this protein a key ingredient for the scaffolding of the NHEJ machinery. However, this threading ability seems unevenly conserved among bacterial Ku. As bacterial Ku differ mainly by their C-terminus, we evaluate the role of this region in the loading and the threading abilities of Bacillus subtilis Ku and the stimulation of the DNA ligase LigD. We identify two distinct sub-regions: a ubiquitous minimal C-terminal region and a frequent basic C-terminal extension. We show that truncation of one or both of these sub-regions in Bacillus subtilis Ku impairs the stimulation of the LigD end joining activity in vitro. We further demonstrate that the minimal C-terminus is required for the Ku-LigD interaction, whereas the basic extension controls the threading and DNA bridging abilities of Ku. We propose that the Ku basic C-terminal extension increases the concentration of Ku near DNA ends, favoring the recruitment of LigD at the break, thanks to the minimal C-terminal sub-region.
    Keywords: Genome Integrity, Repair And Replication;
    ISSN: 03051048
    E-ISSN: 1362-4962
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. Further information can be found on the KOBV privacy pages