Target recognition in tandem WW domains: complex structures for parallel and antiparallel ligand orientation in h-FBP21 tandem WW

Protein-protein interactions often rely on specialized recognition domains, such as WW domains, which bind to specific proline-rich sequences. The specificity of these protein-protein interactions can be increased by tandem repeats, i.e. two WW domains connected by a linker. With a flexible linker, the WW domains can move freely with respect to each other. Additionally, the tandem WW domains can bind in two different orientations to their target sequences. This makes the elucidation of complex structures of tandem WW domains extremely challenging. Here, we identify and characterize two complex structures of the tandem WW domain of human formin-binding protein 21 and a peptide sequence from its natural binding partner, the core-splicing protein SmB/B′. The two structures differ in the ligand orientation, and consequently also in the relative orientation of the two WW domains. We analyze and probe the interactions in the complexes by molecular simulations and NMR experiments. The workflow to identify the complex structures uses molecular simulations, density-based clustering and peptide docking. It is designed to systematically generate possible complex structures for repeats of recognition domains. These stuctures will help us to understand the synergistic and multivalency effects that generate the astonishing versatility and specificity of protein-protein interactions.

Toward E-selective Olefin Metathesis: Computational Design and Experimental Realization of Ruthenium Thio-Indolate Catalysts

The selective transformation of 1-alkenes into E-olefins is a long-standing challenge in olefin metathesis. Density functional theory (DFT) calculations predict high E-selectivity for catalysts incorporating a bidentate, dianionic thio-indolate ligand within a RuXX’(NHC)(py)(= CHR) platform (NHC = N-heterocyclic carbene; py = pyridine). Such complexes are predicted to yield E-olefins by favoring anti-disposed substituents in the transition state expected to be rate-determining: specifically, that for cycloreversion of the metallacyclobutane intermediate. Three pyridine-stabilized catalysts Ru21a-c were synthesized, in which the thio-indolate ligand bears a H, Me, or Ph substituent at the C2 position, and the NHC ligand is the unsaturated imidazoline-2-ylidene Me2IMes (which bears N-mesityl groups and methyl groups on the C4,5 backbone). Single-crystal X-ray diffraction analysis of Ru21c confirms the ligand orientation required for E-selective metathesis, with the thio-indolate sulfur atom binding cis to the NHC, and the indolate nitrogen atom trans to the NHC. However, whereas the new complexes mediated metathetic exchange of their 2-thienylmethylidene ligand in the presence of the common metathesis substrates styrene and allylbenzene, no corresponding self-metathesis products were obtained. Only small amounts of 2-butene (73% (Z)-2-butene) were obtained in self-metathesis of propene using Ru21a. Detailed DFT analysis of this process revealed that product release is surprisingly slow, limiting the reaction rate and explaining the low metathesis activity. With the barrier to dissociation of (Z)-2-butene being lower than that of (E)-2-butene, the calculations also account for the observed Z-selectivity of Ru21a. These findings provide guidelines for catalyst redesign in pursuit of the ambitious goal of E-selective 1-alkene metathesis. Graphic abstract

Determinants of ligand-functionalized DNA nanostructure-cell interactions

Synthesis of ligand-functionalized nanomaterials with control over size, shape and ligand orientation, facilitates the design of tailored nanomedicines for therapeutic purposes. DNA nanotechnology has emerged as a powerful tool to rationally construct two- and three-dimensional nanostructures, enabling site-specific incorporation of protein ligands with control over stoichiometry and orientation. To efficiently target cell surface receptors, exploration of the parameters that modulate cellular accessibility of these nanostructures is essential. In this study we systematically investigate tunable design parameters of antibody-functionalized DNA nanostructures binding to therapeutically relevant receptors. We show that, although the native affinity of antibody-functionalized DNA nanostructures remains unaltered, the absolute number of bound surface receptors is lower compared to soluble antibodies and is mainly governed by nanostructure size and DNA handle location. The obtained results provide key insights in the ability of ligand-functionalized DNA nanostructures to bind surface receptors and yields design rules for optimal cellular targeting.

Histidine orientation in artificial peroxidase regioisomers as determined by paramagnetic NMR shifts

A semi-empirical approach allows determining the His axial-ligand orientation with respect to the porphyrin plane in synthetic heme-peroxidases, for structure/function analysis.

Positional Isomerism in the N^N Ligand: How Much Difference Does a Methyl Group Make in [Cu(P^P)(N^N)]+ Complexes?

The synthesis and structural characterization of 5,6′-dimethyl-2,2′-bipyridine (5,6′-Me2bpy) are reported, along with the preparations and characterizations of [Cu(POP)(5,6′-Me2bpy)][PF6] and [Cu(xantphos)(5,6′-Me2bpy)][PF6] (POP = bis(2-(diphenylphosphanyl)phenyl)ether, xantphos = 4,5-bis(diphenylphosphanyl)-9,9-dimethyl-9H-xanthene). Single-crystal X-ray structure determinations of [Cu(POP)(5,6′-Me2bpy)][PF6] and [Cu(xantphos)(5,6′-Me2bpy)][PF6] confirmed distorted tetrahedral copper(I) coordination environments with the 5-methylpyridine ring of 5,6′-Me2bpy directed towards the (C6H4)2O unit of POP or the xanthene unit of xantphos. In the xantphos case, this preference may be attributed to C–H…π interactions involving both the 6-CH unit and the 5-methyl substituent in the 5-methylpyridine ring and the arene rings of the xanthene unit. 1H NMR spectroscopic data indicate that this ligand orientation is also preferred in solution. In solution and the solid state, [Cu(POP)(5,6′-Me2bpy)][PF6] and [Cu(xantphos)(5,6′-Me2bpy)][PF6] are yellow emitters, and, for powdered samples, photoluminescence quantum yields (PLQYs) are 12 and 11%, respectively, and excited-state lifetimes are 5 and 6 μs, respectively. These values are lower than PLQY and τ values for [Cu(POP)(6,6′-Me2bpy)][PF6] and [Cu(xantphos)(6,6′-Me2bpy)][PF6], and the investigation points to the 6,6′-dimethyl substitution pattern in the bpy ligand being critical for enhancement of the PLQY.

Exopolyhedral Ligand Orientation Controls Diastereoisomer in Mixed-Metal Bis(Carboranes)

Heterobimetallic derivatives of a bis(carborane), [μ7,8-(1′,3′−3′-Cl-3′-PPh3-closo-3′,1′,2′-RhC2B9H10)-2-(p-cymene)-closo-2,1,8-RuC2B9H10] (1) and [μ7,8-(1′,3′−3′-Cl-3′-PPh3-closo-3′,1′,2′-RhC2B9H10)-2-Cp-closo-2,1,8-CoC2B9H10] (2) have been synthesised and characterised, including crystallographic studies. A minor co-product during the synthesis of compound 2 is the new species [8-{8′-2′-H-2′,2′-(PPh3)2-closo-2′,1′,8′-RhC2B9H10}-2-Cp-closo-2,1,8-CoC2B9H10] (3), isolated as a mixture of diastereoisomers. Although, in principle, compounds 1 and 2 could also exist as two diastereoisomers, only one (the same in both cases) is formed. It is suggested that the preferred exopolyhedral ligand orientation in the rhodacarboranes in the non-observed diastereoisomers would lead to unacceptable steric crowding between the PPh3 ligand and either the p-cymene (compound 1) or Cp (compound 2) ligand of the ruthenacarborane or cobaltacarborane, respectively.