Rolf Boelens

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

Tet proteins oxidize 5-methylcytosine (mC) to generate 5-hydroxymethyl (hmC), 5-formyl (fC), and 5-carboxylcytosine (caC). The exact function of these oxidative cytosine bases remains elusive. We applied quantitative mass-spectrometry-based proteomics to identify readers for mC and hmC in mouse embryonic stem cells (mESC), neuronal progenitor cells (NPC), and adult mouse brain tissue. Readers for these modifications are only partially overlapping, and some readers, such as Rfx proteins, display strong specificity. Interactions are dynamic during differentiation, as for example evidenced by the mESC-specific binding of Klf4 to mC and the NPC-specific binding of Uhrf2 to hmC, suggesting specific biological roles for mC and hmC. Oxidized derivatives of mC recruit distinct transcription regulators as well as a large number of DNA repair proteins in mouse ES cells, implicating the DNA damage response as a major player in active DNA demethylation.

A protein structure from nuclear magnetic resonance data. lac repressor headpiece.

A procedure is described to determine the three-dimensional structure of biomolecules from nuclear magnetic resonance data. This procedure combines model building with a restrained molecular dynamics algorithm, in which distance information from nuclear Overhauser effects is incorporated in the form of pseudo potentials. The method has been applied to the N-terminal DNA-binding domain or headpiece (amino acid residues 1 to 51) of the lac repressor from Escherichia coli, for which no crystal structure is available. The relative orientation of the three helices of the headpiece is similar to that of the three homologous helices found in the cI repressor of bacteriophage lambda.

The DNA-binding domain of HIV-1 integrase has an SH3-like fold

We have determined the solution structure of the DNA-binding domain of HIV-1 integrase by nuclear magnetic resonance spectroscopy. In solution, this carboxy-terminal region of integrase forms a homodimer, consisting of two structures that closely resemble Src-homology 3 (SH3) domains. Lys 264, previously identified by mutagenesis studies to be important for DNA binding of the integrase, as well as several adjacent basic amino acids are solvent exposed. The identification of an SH3-like domain in integrase provides a new potential target for drug design.

Iterative procedure for structure determination from proton-proton NOEs using a full relaxation matrix approach. Application to a DNA octamer

Abstract A method is proposed, called the iterative relaxation matrix approach (IRMA), for the structure determination of biomolecules in solution based on 2D NOE data. Proton-proton distances are determined in a way in which indirect magnetization transfer (spin diffusion) is taken fully into account. In this method experimental NOEs are combined with calculated NOE values based on a molecular model. Back-transformation of this mixed NOE matrix gives a relaxation matrix which provides a better estimation of the cross-relaxation rates than can be obtained directly from the NOE cross peaks. From the cross-relaxation rates distance constraints can be derived, which are used in restrained molecular dynamics calculations to obtain an improved molecular model. The iteration cycle can be repeated until all experimental NOE values are satisfactorily explained. The method was tested with a DNA octamer, d(GCGTTGCG)·d(CGCAACGC).

Determination of biomolecular structures from proton-proton NOE's using a relaxation matrix approach

Abstract A method is proposed for the structure determination of biomolecules in solution based on 2D NOE data in which indirect magnetization transfer (spin diffusion) is taken into account. In this method experimental NOEs are supplemented with calculated NOEs based on a molecular model. Back transformation of this mixed NOE matrix gives a relaxation matrix which provides a better estimation for the cross-relaxation rates than can be obtained directly from the NOE cross-peaks. From the cross-relaxation rates distance constraints can be derived, which can be used in distance geometry and restrained molecular dynamics calculations to obtain an improved molecular model. The procedure can be repeated until all experimental NOEs are satisfactorily explained.

Identification of a ubiquitin-protein ligase subunit within the CCR4-NOT transcription repressor complex

The RING finger protein CNOT4 is a component of the CCR4–NOT complex. This complex is implicated in repression of RNA polymerase II transcription. Here we demonstrate that CNOT4 functions as a ubiquitin–protein ligase (E3). We show that the unique C4C4 RING domain of CNOT4 interacts with a subset of ubiquitin‐conjugating enzymes (E2s). Using NMR spectroscopy, we detail the interaction of CNOT4 with UbcH5B and characterize RING residues that are critical for this interaction. CNOT4 acts as a potent E3 ligase in vitro. Mutations that destabilize the E2–E3 interface abolish this activity. Based on these results, we present a model of how E3 ligase function within the CCR4–NOT complex relates to transcriptional regulation.

New insights into the structure and composition of technical lignins: a comparative characterisation study

Detailed insight into the structure and composition of industrial (technical) lignins is needed to devise efficient thermal, bio- or chemocatalytic valorisation strategies. Six such technical lignins covering three main industrial pulping methods (Indulin AT Kraft, Protobind 1000 soda lignin and Alcell, poplar, spruce and wheat straw organosolv lignins) were comprehensively characterised by lignin composition analysis, FT-IR, pyrolysis-GC-MS, quantitative 31P and 2D HSQC NMR analysis and molar mass distribution by Size Exclusion Chromatography (SEC). A comparison of nine SEC methods, including the first analysis of lignins with commercial alkaline SEC columns, showed molar masses to vary considerably, allowing some recommendations to be made. The lignin molar mass decreased in the order: Indulin Kraft > soda P1000 > Alcell > OS-W ∼ OS-P ∼ OS-S, regardless of the SEC method chosen. Structural identification and quantification of aromatic units and inter-unit linkages indicated that all technical lignins, including the organosolv ones, have considerably been degraded and condensed by the pulping process. Importantly, low amounts of β- ether linkages were found compared to literature values for protolignin and lignins obtained by other, milder isolation processes. Stilbenes and ether furfural units could also be identified in some of the lignins. Taken together, the insights gained in the structure of the technical lignins, in particular, the low β-O-4 contents, carry implications for the design of lignin valorisation strategies including (catalytic) depolymerisation and material applications.

Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility

Intrinsic flexibility of DNA has hampered the development of efficient protein−DNA docking methods. In this study we extend HADDOCK (High Ambiguity Driven DOCKing) [C. Dominguez, R. Boelens and A. M. J. J. Bonvin (2003) J. Am. Chem. Soc. 125, 1731–1737] to explicitly deal with DNA flexibility. HADDOCK uses non-structural experimental data to drive the docking during a rigid-body energy minimization, and semi-flexible and water refinement stages. The latter allow for flexibility of all DNA nucleotides and the residues of the protein at the predicted interface. We evaluated our approach on the monomeric repressor−DNA complexes formed by bacteriophage 434 Cro, the Escherichia coli Lac headpiece and bacteriophage P22 Arc. Starting from unbound proteins and canonical B-DNA we correctly predict the correct spatial disposition of the complexes and the specific conformation of the DNA in the published complexes. This information is subsequently used to generate a library of pre-bent and twisted DNA structures that served as input for a second docking round. The resulting top ranking solutions exhibit high similarity to the published complexes in terms of root mean square deviations, intermolecular contacts and DNA conformation. Our two-stage docking method is thus able to successfully predict protein−DNA complexes from unbound constituents using non-structural experimental data to drive the docking.

Structural and dynamic changes of photoactive yellow protein during its photocycle in solution.

Light irradiation of photoactive yellow protein (PYP) induces a photocycle, in which red-shifted (pR) and blue-shifted (pB) intermediates have been characterized. An NMR study of the long-lived pB intermediate now reveals that it exhibits a large degree of disorder and exists as a family of multiple conformers that exchange on a millisecond time scale. This shows that the behavior of PYP in solution is different from what has been observed in the crystalline state. Furthermore, differential refolding to ground state pG is observed, whereby the central β-sheet and parts of the helical structure are formed first and the region around the chromophore at a later stage.

Data-driven docking for the study of biomolecular complexes

With the amount of genetic information available, a lot of attention has focused on systems biology, in particular biomolecular interactions. Considering the huge number of such interactions, and their often weak and transient nature, conventional experimental methods such as X‐ray crystallography and NMR spectroscopy are not sufficient to gain structural insight into these. A wealth of biochemical and/or biophysical data can, however, readily be obtained for biomolecular complexes. Combining these data with docking (the process of modeling the 3D structure of a complex from its known constituents) should provide valuable structural information and complement the classical structural methods. In this review we discuss and illustrate the various sources of data that can be used to map interactions and their combination with docking methods to generate structural models of the complexes. Finally a perspective on the future of this kind of approach is given.