27 results match your criteria: "Charles Tanford Protein Centre[Affiliation]"

MS -Pushing the Limits for Biomolecular Mass Spectrometry.

J Am Soc Mass Spectrom

January 2025

Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany.

Electrospray mass spectrometry has become indispensable in many disciplines including the classic "omics" techniques such as proteomics or lipidomics, as well as other life science applications in molecular, cellular, and structural biology. However, a limiting factor that often arises for the detection of biomolecular analytes is their poor ionization efficiency in the ion source. Here, we present an add-on device for the electrospray source, termed MS (MS Spectral Impurity Eliminator & Value Enhancer), which is placed between the electrospray needle and the cone of the mass spectrometer.

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Aqueous Ionic Liquid Mixtures as Minimal Models of Lipid Bilayer Membranes.

ACS Biomater Sci Eng

August 2024

Martin Luther University Halle-Wittenberg, Institute of Chemistry, Physical Chemistry - Complex Self-Organizing Systems, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany.

We introduce aqueous ionic liquid (IL) mixtures, specifically mixtures of 1-butyl-3-imidazoliumtetrafluoroborate (BMImBF), with water as a minimal model of lipid bilayer membranes. Imidazolium-based ILs are known to form clustered nanoscale structures in which local inhomogeneities, micellar or lamellar structures, are formed to shield hydrophobic parts of the cation from the polar cosolvent (water). To investigate these nanostructures, dynamic light scattering (DLS) on samples with different mixing ratios of water and BMImBF was performed.

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For protein evaluation of feedstuffs for ruminants, the protease test provides a solely enzymatic method for estimating ruminal protein degradation. Since plant proteins are often structured in carbohydrate complexes, the use of carbohydrase during the test might improve its accuracy. It is advisable to co-incubate protease and carbohydrase, risking that the carbohydrase activity is reduced under the influence of the protease.

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GPR55 is involved in many physiological and pathological processes. In cancer, GPR55 has been described to show accelerating and decelerating effects in tumor progression resulting from distinct intracellular signaling pathways. GPR55 becomes activated by LPI and various plant-derived, endogenous, and synthetic cannabinoids.

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Deciphering Solution and Gas-Phase Interactions between Peptides and Lipids by Native Mass Spectrometry.

Anal Chem

November 2023

Interdisciplinary Research Centre HALOmem, Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany.

Many biological processes depend on the interactions between proteins and lipids. Accordingly, the analysis of protein-lipid complexes has become increasingly important. Native mass spectrometry is often used to identify and characterize specific protein-lipid interactions.

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Mass spectrometry uncovers intermediates and off-pathway complexes for SNARE complex assembly.

Commun Biol

February 2023

Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany.

The SNARE complex assembles from vesicular Synaptobrevin-2 as well as Syntaxin-1 and SNAP25 both anchored to the presynaptic membrane. It mediates fusion of synaptic vesicles with the presynaptic plasma membrane resulting in exocytosis of neurotransmitters. While the general sequence of SNARE complex formation is well-established, our knowledge on possible intermediates and stable off-pathway complexes is incomplete.

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Teaching product operators using the Vega diagram.

Solid State Nucl Magn Reson

December 2022

Universität Leipzig, Institut für Medizinische Physik und Biophysik, Härtelstr. 16-18, 04107, Leipzig, Germany; Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, the Netherlands.

We all will remember Shimon Vega (1942-2021) as wonderful human and scientist. Paramount examples of his scientific work are quoted in this special issue dedicated to his memory. This article is dedicated to remember Shimon Vega as a fantastic teacher.

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Backbone and side chain resonance assignment of the intrinsically disordered human DBNDD1 protein.

Biomol NMR Assign

October 2022

Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany.

The dysbindin domain-containing protein 1 (DBNDD1) is a conserved protein among higher eukaryotes whose structure and function are poorly investigated so far. Here, we present the backbone and side chain nuclear magnetic resonance assignments for the human DBNDD1 protein. Our chemical-shift based secondary structure analysis reveals the human DBNDD1 as an intrinsically disordered protein.

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Even though the human genome project showed that our DNA contains a mere 20,000 to 25,000 protein coding genes, an unexpectedly large number of these proteins remain functionally uncharacterized. A structural characterization of these "unknown" proteins may help to identify possible cellular tasks. We therefore used a combination of bioinformatics and nuclear magnetic resonance spectroscopy to structurally de-orphanize one of these gene products, the 108 amino acid human uncharacterized protein CXorf51A.

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The highly infectious disease COVID-19 caused by the SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail.

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N NMR studies provide insights into physico-chemical properties of room-temperature ionic liquids.

Phys Chem Chem Phys

June 2021

Martin Luther University Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle/S., Germany.

Ionic liquids (ILs) have gained a lot of attention as alternative solvents in many fields of science in the last two decades. It is known that the type of anion has a significant influence on the macroscopic properties of the IL. To gain insights into the molecular mechanisms responsible for these effects it is important to characterize these systems at the microscopic level.

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Cross-linking mass spectrometry uncovers protein interactions and functional assemblies in synaptic vesicle membranes.

Nat Commun

February 2021

Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany.

Article Synopsis
  • Synaptic vesicles store neurotransmitters and fuse with the nerve terminal's pre-synaptic membrane in response to action potentials, but the interactions between proteins in their membranes are not well understood.
  • This study uses cross-linking mass spectrometry to analyze protein interactions in synaptic vesicles without requiring antibodies, producing a detailed protein network with various functional groups.
  • The research highlights Synaptobrevin-2 as a key protein involved in multiple interactions and successfully distinguishes between transient 'crowding' interactions and stable protein connections within the vesicle membrane.
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Exploring Phosphoinositide Binding Using Native Mass Spectrometry.

Methods Mol Biol

March 2021

Interdisciplinary research center HALOmem, Institute for Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle, Germany.

Phosphoinositides interact with proteins to fulfill various functions in the cell. In many cases, they specifically recruit peripheral membrane proteins to biological membranes. The analysis of their interactions with proteins is therefore essential for understanding the underlying processes.

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Death-associated protein 1 (DAP1) is a proline-rich cytoplasmatic protein highly conserved in most eukaryotes. It has been reported to be involved in controlling cell growth and migration, autophagy and apoptosis. The presence of human DAP1 is associated to a favourable prognosis in different types of cancer.

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Trypsiligase-Catalyzed Labeling of Proteins on Living Cells.

Chembiochem

April 2021

Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany.

Fluorescent fusion proteins are powerful tools for studying biological processes in living cells, but universal application is limited due to the voluminous size of those tags, which might have an impact on the folding, localization or even the biological function of the target protein. The designed biocatalyst trypsiligase enables site-directed linkage of small-sized fluorescence dyes on the N terminus of integral target proteins located in the outer membrane of living cells through a stable native peptide bond. The function of the approach was tested by using the examples of covalent derivatization of the transmembrane proteins CD147 as well as the EGF receptor, both presented on human HeLa cells.

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Proper base-pairing of a miRNA with its target mRNA is a key step in miRNA-mediated mRNA repression. RNA remodelling by RNA-binding proteins (RBPs) can improve access of miRNAs to their target mRNAs. The largest isoform p45 of the RBP AUF1 has previously been shown to remodel viral or AU-rich RNA elements.

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Validation strategies for antibodies targeting modified ribonucleotides.

RNA

October 2020

Regensburg Center for Biochemistry, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany.

Chemical modifications are found on almost all RNAs and affect their coding and noncoding functions. The identification of mA on mRNA and its important role in gene regulation stimulated the field to investigate whether additional modifications are present on mRNAs. Indeed, modifications including mA, mC, mG, 2'-OMe, and Ψ were detected.

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RNA Remodeling by RNA Chaperones Monitored by RNA Structure Probing.

Methods Mol Biol

June 2021

Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany.

RNA structure probing enables the characterization of RNA secondary structures by established procedures such as the enzyme- or chemical-based detection of single- or double-stranded regions. A specific type of application involves the detection of changes of RNA structures and conformations that are induced by proteins with RNA chaperone activity. This chapter outlines a protocol to analyze RNA structures in vitro in the presence of an RNA-binding protein with RNA chaperone activity.

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Continuous Activity Assay for HDAC11 Enabling Reevaluation of HDAC Inhibitors.

ACS Omega

November 2019

Department of Enzymology, Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany.

Histone deacetylase 11 (HDAC11) preferentially removes fatty acid residues from lysine side chains in a peptide or protein environment. Here, we report the development and validation of a continuous fluorescence-based activity assay using an internally quenched TNFα-derived peptide derivative as a substrate. The threonine residue in the +1 position was replaced by the quencher amino acid 3'-nitro-l-tyrosine and the fatty acyl moiety substituted by 2-aminobenzoylated 11-aminoundecanoic acid.

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Decision-Making in Cascade Complexes Harboring crRNAs of Altered Length.

Cell Rep

September 2019

Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany. Electronic address:

The multi-subunit type I CRISPR-Cas surveillance complex Cascade uses its crRNA to recognize dsDNA targets. Recognition involves DNA unwinding and base-pairing between the crRNA spacer region and a complementary DNA strand, resulting in formation of an R-loop structure. The modular Cascade architecture allows assembly of complexes containing crRNAs with altered spacer lengths that promise increased target specificity in emerging biotechnological applications.

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The BOR proteins are integral membrane transporters which mediate efflux of boron. Structures of two BOR family members from and indicate that the proteins exist as dimers. However, it remains unclear whether dimer formation is dependent on protein-lipid interactions or whether the dimer is the functional form of the protein.

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Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. Here we present structures of the neddylated and deneddylated CSN-CRL2 complexes by combining single-particle cryo-electron microscopy (cryo-EM) with chemical cross-linking mass spectrometry (XL-MS).

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[NiFe]-hydrogenase (Hyd) 2 of Escherichia coli has been proposed to generate proton motive force during H -oxidation, which it is dependent on if cells are incubated anaerobically with glycerol to drive reverse H -production. The integral membrane subunit HybB is required for proton transfer (PT) by Hyd-2 but has no cofactor. To provide evidence for PT by HybB, we analyzed the roles of conserved amino acid residues in a predicted proton channel.

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Instrument response of phosphatidylglycerol lipids with varying fatty acyl chain length in nano-ESI shotgun experiments.

Chem Phys Lipids

September 2019

Interdisciplinary research centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany. Electronic address:

In recent years, lipid quantification gained importance. In most cases, this is achieved by spiking the lipid mixture with deuterated standard lipids or lipid analogues that differ in chain length when compared with the natural lipid components. Usually, conventional ESI is employed requiring sample amounts which are not always available.

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POLIII-derived non-coding RNAs acting as scaffolds and decoys.

J Mol Cell Biol

October 2019

Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle, Germany.

A large variety of eukaryotic small structured POLIII-derived non-coding RNAs (ncRNAs) have been described in the past. However, for only few, e.g.

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