Showing papers by "Luc Brunsveld published in 2009"

Bioactivity-guided mapping and navigation of chemical space

Abstract: The structure- and chemistry-based hierarchical organization of library scaffolds in tree-like arrangements provides a valid, intuitive means to map and navigate chemical space. We demonstrate that scaffold trees built using bioactivity as the key selection criterion for structural simplification during tree construction allow efficient and intuitive mapping, visualization and navigation of the chemical space defined by a given library, which in turn allows correlation of this chemical space with the investigated bioactivity and further compound design. Brachiation along the branches of such trees from structurally complex to simple scaffolds with retained yet varying bioactivity is feasible at high frequency for the five major pharmaceutically relevant target classes and allows for the identification of new inhibitor types for a given target. We provide proof of principle by identifying new active scaffolds for 5-lipoxygenase and the estrogen receptor ER.

A Supramolecular Polymer as a Self‐Assembling Polyvalent Scaffold

Abstract: Bindung an Bakterien: Diskotische Molekule aggregieren zu columnaren supramolekularen Polymeren, die uber Mannoseeinheiten, die an ihrer Peripherie angebracht sind (orange; siehe Bild), eine starke polyvalente Bindung an Bakterien zeigen. Die reversible Bildung der supramolekularen Polymere ermoglicht ein einfaches Mischen unterschiedlich substituierter Monomere und die Optimierung der Bakterienaggregation.

Influence of the lipidation motif on the partitioning and association of N-ras in model membrane subdomains

Abstract: In a combined chemical biological and biophysical approach using time-lapse tapping-mode atomic force microscopy, we studied the partitioning of differently lipidated N-Ras proteins with various membrane-localization motifs into lipid domains of canonical model raft mixtures. The results provide direct evidence that partitioning of N-Ras occurs preferentially into liquid-disordered lipid domains, independent of the lipid anchor system. N-Ras proteins bearing at least one farnesyl group have a comparable membrane partitioning behavior and show diffusion of the protein into the liquid-disordered/liquid-ordered phase boundary region, thus leading to a decrease of the unfavorable line tension between domains. In addition, except for the monofarnesylated N-Ras, strong intermolecular interactions foster self-association and formation of nanoclusters at the domain boundaries and may serve as an important vehicle for association processes and nanoclustering, which has also been observed in in vivo studies. No significant changes of the localization between GDP- and GTP-loaded N-Ras could be detected. Conversely, the nonbiological dual-hexadecylated N-Ras exhibits a time-independent incorporation into the bulk liquid-disordered phase to maintain high conformational entropy of its lipid chains.

Modulation of Protein Dimerization by a Supramolecular Host–Guest System

Abstract: Two sets of cyan and yellow fluorescent proteins, monomeric analogues, and analogues with a weak affinity for dimerization were functionalized with supramolecular host–guest molecules by expressed protein ligation. The host–guest elements induce selective assembly of the monomeric variants into a supramolecular heterodimer. For the second set of analogues, the supramolecular host–guest system acts in cooperation with the intrinsic affinity between the two proteins, resulting in the induction of a selective protein–protein heterodimerization at a more dilute concentration. Additionally, the supramolecular host–guest system allows locking of the two proteins in a covalent heterodimer through the facilitated and selective formation of a reversible disulfide linkage. For the monomeric analogues this results in a strong increase of the energy transfer between the proteins. The protein heterodimerization can be reversed in a stepwise fashion. The trajectory of the disassembly process differs for the monomeric and dimerizing set of proteins. The results highlight that supramolecular elements connected to proteins can both be used to facilitate the interaction between two proteins without intrinsic affinity and to stabilize weak protein–protein interactions at concentrations below those determined by the actual affinity of the proteins alone. The subsequent covalent linkage between the proteins generates a stable protein dimer as a single species. The action of the supramolecular elements in concert with the proteins thus allows the generation of protein architectures with specific properties and compositions.

Mapping the Isoprenoid Binding Pocket of PDEδ by a Semisynthetic, Photoactivatable N-Ras Lipoprotein

Abstract: Biologically functional Ras isoforms undergo post-translational modifications starting with farnesylation of the most C-terminal cysteine. Combined with further processing steps, this isoprenylation allows for the anchoring of these proteins in endomembranes, where signal transduction events take place. The specific localization is subject to dynamic regulation and assumed to modulate the activity of Ras proteins by governing their spatiotemporal distribution. The d subunit of phosphodiesterase (PDEd) has attracted attention as a solubilization factor of isoprenylated Ras. In this study, we demonstrate that critical residues in the putative isoprenoid pocket of PDEd can be mapped by coupling with a semisynthetic N-Ras lipoprotein in which the native farnesyl group of the processed protein was replaced by a photoactivatable geranyl benzophenone moiety. The crosslinked product included parts of s-sheet 9 of PDEd, which contains the highly conserved amino acids V145 and L147. Modeling of the PDEd-geranyl benzophenone (GerBP) complex supports the conclusion that the photolabeled sequence is embedded in the putative isoprenoid pocket of PDEd. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.