A5052112949- DNA and Nucleic Acid Chemistry
- Protein Structure and Dynamics
- Advanced NMR Techniques and Applications
- Retinoids in leukemia and cellular processes
- Estrogen and related hormone effects
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Enzyme Structure and Function
- DNA Repair Mechanisms
- Genomics and Chromatin Dynamics
- Bacteriophages and microbial interactions
- Solid-state spectroscopy and crystallography
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- RNA modifications and cancer
- Ubiquitin and proteasome pathways
- Nuclear Receptors and Signaling
- Viral Infectious Diseases and Gene Expression in Insects
- Genetics and Neurodevelopmental Disorders
- Electron Spin Resonance Studies
- Peptidase Inhibition and Analysis
- Monoclonal and Polyclonal Antibodies Research
- Muon and positron interactions and applications
- Protein purification and stability
- Carbohydrate Chemistry and Synthesis
Utrecht University
2015-2025
Institut de Biologia Molecular de Barcelona
2011
Hubrecht Institute for Developmental Biology and Stem Cell Research
1992-1999
Wageningen University & Research
1991
Translational initiation factor 2 (IF2) is a guanine nucleotide-binding protein that can bind guanosine 3′,5′-(bis) diphosphate (ppGpp), an alarmone involved in stringent response bacteria. In cells growing under optimal conditions, the GTP concentration very high, and of ppGpp low. However, stress may decline by as much 50%, attain levels comparable to those GTP. Here we show IF2 binds at same site with similar affinity Thus, be considered two alternative physiologically relevant ligands....
Elucidating at atomic level how proteins interact and are chemically modified in cells represents a leading frontier structural biology. We have developed tailored solid-state NMR spectroscopic approach that allows studying protein structure inside human under high-sensitivity dynamic nuclear polarization (DNP) conditions. demonstrate the method using ubiquitin (Ub), which is critically involved cellular functioning. Our results pave way for studies of larger or complexes cells, remained...
Protein–protein complexes orchestrate most cellular processes such as transcription, signal transduction and apoptosis. The factors governing their affinity remain elusive however, especially when it comes to describing dissociation rates (koff). Here we demonstrate that, next direct contributions from the interface, non-interacting surface (NIS) also plays an important role in binding affinity, polar charged residues. Their percentage on NIS is conserved over orthologous indicating...
We describe isolation and characterization of the bovine ortholog POU5F1 (bPOU5F1) encoding octamer-binding transcription factor-4 (Oct-4). The organization bPOU5F1 is similar to its human murine orthologs, it shares 90.6% 81.7% overall identity at protein level, respectively. Transient transfection luciferase reporter constructs in P19 embryonal carcinoma cells demonstrated that has a functional promoter contains two enhancer elements, which one repressed by retinoic acid. was mapped major...
Producing soluble proteins in Escherichia coli is still a major bottleneck for structural proteomics. Therefore, screening expression on small scale an attractive way of identifying constructs that are likely to be amenable analysis. A variety expression-screening methods have been developed within the Structural Proteomics In Europe (SPINE) consortium and assist further refinement such approaches, eight laboratories participating network benchmarked their protocols. For this study,...
Abstract Quantitative evaluation of binding affinity changes upon mutations is crucial for protein engineering and drug design. Machine learning‐based methods are gaining increasing momentum in this field. Due to the limited number experimental data, using a small sensitive predictive features vital generalization robustness such machine learning methods. Here we introduce fast reliable predictor single point mutation, based on random forest approach. Our method, iSEE, uses i nterface S...
We show that the polarising agent SNAPol-1 enters human cells yielding 800 MHz DNP solid-state NMR data of remarkable sensitivity & resolution thereby revealing structural heterogeneity ubiquitin at atomic scale and with sub-cellular specificity.
Abstract Sensitivity enhanced dynamic nuclear polarization solid‐state NMR is emerging as a powerful technique for probing the structural properties of conformationally homogenous and heterogenous biomolecular species irrespective size at atomic resolution within their native environments. Herein we detail advancements that have made acquiring such data, specifically confines intact bacterial eukaryotic cell reality further discuss type information can presently be garnered by technique's...
Solid-state NMR spectroscopy (ssNMR) has made significant progress towards the study of membrane proteins in their native cellular membranes. However, reduced spectroscopic sensitivity and high background signal levels can complicate these experiments. Here, we describe a method for ssNMR to specifically label single protein by repressing endogenous expression with rifampicin. Our results demonstrate that treatment E. coli rifampicin during induction recombinant reduces signals different...
Mitochondria are central to cellular bioenergetics, with the unique ability translate and transcribe a subset of their own proteome. Given critical importance energy production, mitochondria seem utilize higher-order nucleic acid structures regulate gene expression, much like nuclei. Herein, we introduce tailored approach probe formation such structures, specifically G-quadruplexes, within intact using sensitivity-enhanced dynamic nuclear polarization-supported solid-state NMR (DNP-ssNMR)....
Mitochondria are central to cellular bioenergetics, with the unique ability translate and transcribe a subset of their own proteome. Given critical importance energy production, mitochondria seem utilize higher‐order nucleic acid structures regulate gene expression, much like nuclei. Herein, we introduce tailored approach probe formation such structures, specifically G‐quadruplexes, within intact using sensitivity‐enhanced dynamic nuclear polarization‐supported solid‐state NMR (DNP‐ssNMR)....
Retinoids regulate gene expression via nuclear retinoic acid receptors, the RARs and RXRs. To investigate functions of retinoid receptors during early neural development, we expressed a dominant negative RARbeta in Xenopus embryos. We obtained evidence that specifically inhibits RAR/RXR heterodimer-mediated, but not RXR homodimer-mediated, transactivation. Both all-trans- 9-cis-RA-induced teratogenesis were, however, efficiently opposed by ectopic RARbeta, indicating only transactivation is...
Herpes simplex virion protein 16 (VP16) contains two strong activation regions that can independently and cooperatively activate transcription in vivo. We have identified the residues involved interaction with human transcriptional coactivator positive cofactor 4 (PC4) general factor TFIIB. NMR biochemical experiments revealed both VP16 are required for undergo a conformational transition from random coil to α-helix upon binding its target PC4. The is strongly electrostatically driven PC4...
The implementation of high-throughput (HTP) cloning and expression screening in Escherichia coli by 14 laboratories the Structural Proteomics In Europe (SPINE) consortium is described. Cloning efficiencies greater than 80% have been achieved for three non-ligation-based techniques used, namely Gateway, ligation-indendent PCR products (LIC-PCR) In-Fusion, with LIC-PCR emerging as most cost-effective. On average, two constructs made each approximately 1700 protein targets selected SPINE...
Abstract Elucidating at atomic level how proteins interact and are chemically modified in cells represents a leading frontier structural biology. We have developed tailored solid‐state NMR spectroscopic approach that allows studying protein structure inside human under high‐sensitivity dynamic nuclear polarization (DNP) conditions. demonstrate the method using ubiquitin (Ub), which is critically involved cellular functioning. Our results pave way for studies of larger or complexes cells,...
High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the dimeric Escherichia coli Lac repressor. In absence ligands, dimer exists in a dynamic equilibrium DNA-bound and inducer-bound conformations. Binding either effector shifts this toward bound state. Analysis ternary complex repressor, operator DNA, inducer shows how adding results changes that disrupt interdomain contacts binding DNA domains turn leads destabilization...