Publications by authors named "Vandenameele J"

Article Synopsis
  • Transcriptomes are made up of various RNA classes that have important but often unclear functions, and their deregulation is linked to many diseases.
  • The study focused on the RanBP2-type Zinc Finger (ZF) domain to understand single-stranded RNA-binding proteins (RBPs), revealing that different ZFs have similar sequence specificity despite variations in RNA-binding residues.
  • A new 6-ZF chimeric protein was created to improve targeting of longer RNA sequences, successfully recognizing a specific 20-nucleotide target both in tests and living cells, highlighting the potential of ZFs in RBP design despite challenges in engineering specificity.
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Six 1',5'-anhydrohexitol uridine triphosphates were synthesized with aromatic substitutions appended via a carboxamide linker to the 5-position of their bases. An improved method for obtaining such 5-substituted hexitol nucleosides and nucleotides is described. The incorporation profile of the nucleotide analogues into a DNA duplex overhang using recently evolved XNA polymerases is compared.

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A mannose binding jacalin-related lectin from Ananas comosus stem (AcmJRL) was purified and biochemically characterized. This lectin is homogeneous according to native, SDS-PAGE and N-terminal sequencing and the theoretical molecular mass was confirmed by ESI-Q-TOF-MS. AcmJRL was found homodimeric in solution by size-exclusion chromatography.

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Recent advances in transcriptome sequencing and analysis have revealed the complexity of the human genome. The majority (≈ 98%) of cellular transcripts is not translated into proteins and represents a vast, unchartered world of functional non-coding RNAs. Most of them adopt a well-defined three-dimensional structure to achieve their biological functions.

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Article Synopsis
  • The paper proposes using infrared imaging to analyze protein microarrays without needing any labels like enzymes or fluorescence, allowing for simultaneous data on various protein characteristics.
  • High-density protein spots with about 100 pg of protein were created, enabling the capture of detailed infrared spectra from each pixel of the images produced by infrared detectors.
  • The study further explains how to manage different types of noise in the infrared spectra to achieve high-quality results and concludes that the protein secondary structure remains intact during the microarray process.
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Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1.

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Class A β-lactamases (260-280 amino acids; M ( r ) ~ 29,000) are among the largest proteins studied in term of their folding properties. They are composed of two structural domains: an all-α domain formed by five to eight helices and an α/β domain consisting of a five-stranded antiparallel β-sheet covered by three to four α-helices. The α domain (~150 residues) is made up of the central part of the polypeptide chain whereas the α/β domain (111-135 residues) is constituted by the N- and C-termini of the protein.

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Metallo-beta-lactamase (MBL)-producing bacteria are emerging worldwide and represent a formidable threat to the efficacy of relevant beta-lactams, including carbapenems, expanded-spectrum cephalosporins, and beta-lactamase inactivator/beta-lactam combinations. VIM-2 is currently the most widespread MBL and represents a primary target for MBL inhibitor research, the clinical need for which is expected to further increase in the future. Using a saturation mutagenesis approach, we probed the importance of four residues (Phe-61, Ala-64, Tyr-67, and Trp-87) located close to the VIM-2 active site and putatively relevant to the enzyme activity based on structural knowledge of the enzyme and on structure-activity relationships of the subclass B1 MBLs.

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Article Synopsis
  • Class A beta-lactamases are used as models to study how large proteins fold, particularly focusing on the role of a specific cis peptide bond at their active site.
  • The study examines how various beta-lactamases differ in this folding process due to varying structures around the cis peptide bond, influencing their refolding and enzymatic activity recovery.
  • The results indicate that while protein folding can occur with the peptide bond in an incorrect trans form, the conversion to the correct cis form is essential for restoring enzyme function, highlighting the importance of peptide bond isomerization in the overall folding kinetics.
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Use of the MagNA Pure LC Total Nucleic Acid Isolation Kit-Large Volume in conjunction with the TRUGENE HIV-1 Genotyping Kit yielded consistent, interpretable sequence data from 1-mL plasma preparations containing HIV-1 RNA concentrations of > or =400 copies/mL. This finding was confirmed in 18 of 24 low-titer clinical specimens.

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