Klaartje Houben

EGFR Dynamics Change during Activation in Native Membranes as Revealed by NMR

The epidermal growth factor receptor (EGFR) represents one of the most common target proteins in anti-cancer therapy. To directly examine the structural and dynamical properties of EGFR activation by the epidermal growth factor (EGF) in native membranes, we have developed a solid-state nuclear magnetic resonance (ssNMR)-based approach supported by dynamic nuclear polarization (DNP). In contrast to previous crystallographic results, our experiments show that the ligand-free state of the extracellular domain (ECD) is highly dynamic, while the intracellular kinase domain (KD) is rigid. Ligand binding restricts the overall and local motion of EGFR domains, including the ECD and the C-terminal region. We propose that the reduction in conformational entropy of the ECD by ligand binding favors the cooperative binding required for receptor dimerization, causing allosteric activation of the intracellular tyrosine kinase.

An Efficient Labelling Approach to Harness Backbone and Side‐Chain Protons in 1H‐Detected Solid‐State NMR Spectroscopy

1H-detection can greatly improve spectral sensitivity in biological solid-state NMR (ssNMR), thus allowing the study of larger and more complex proteins. However, the general requirement to perdeuterate proteins critically curtails the potential of 1H-detection by the loss of aliphatic side-chain protons, which are important probes for protein structure and function. Introduced herein is a labelling scheme for 1H-detected ssNMR, and it gives high quality spectra for both side-chain and backbone protons, and allows quantitative assignments and aids in probing interresidual contacts. Excellent 1H resolution in membrane proteins is obtained, the topology and dynamics of an ion channel were studied. This labelling scheme will open new avenues for the study of challenging proteins by ssNMR.

Initial Carbon–Carbon Bond Formation during the Early Stages of the Methanol-to-Olefin Process Proven by Zeolite-Trapped Acetate and Methyl Acetate

Abstract Methanol‐to‐olefin (MTO) catalysis is a very active field of research because there is a wide variety of sometimes conflicting mechanistic proposals. An example is the ongoing discussion on the initial C−C bond formation from methanol during the induction period of the MTO process. By employing a combination of solid‐state NMR spectroscopy with UV/Vis diffuse reflectance spectroscopy and mass spectrometry on an active H‐SAPO‐34 catalyst, we provide spectroscopic evidence for the formation of surface acetate and methyl acetate, as well as dimethoxymethane during the MTO process. As a consequence, new insights in the formation of the first C−C bond are provided, suggesting a direct mechanism may be operative, at least in the early stages of the MTO reaction.

1H-Detected Solid-State NMR Studies of Water-Inaccessible Proteins In Vitro and In Situ

Abstract 1H detection can significantly improve solid‐state NMR spectral sensitivity and thereby allows studying more complex proteins. However, the common prerequisite for 1H detection is the introduction of exchangeable protons in otherwise deuterated proteins, which has thus far significantly hampered studies of partly water‐inaccessible proteins, such as membrane proteins. Herein, we present an approach that enables high‐resolution 1H‐detected solid‐state NMR (ssNMR) studies of water‐inaccessible proteins, and that even works in highly complex environments such as cellular surfaces. In particular, the method was applied to study the K+ channel KcsA in liposomes and in situ in native bacterial cell membranes. We used our data for a dynamic analysis, and we show that the selectivity filter, which is responsible for ion conduction and highly conserved in K+ channels, undergoes pronounced molecular motion. We expect this approach to open new avenues for biomolecular ssNMR.

Nuclear magnetic resonance (NMR) applied to membrane-protein complexes

Increasing evidence suggests that most proteins occur and function in complexes rather than as isolated entities when embedded in cellular membranes. Nuclear magnetic resonance (NMR) provides increasing possibilities to study structure, dynamics and assembly of such systems. In our review, we discuss recent methodological progress to study membrane-protein complexes (MPCs) by NMR, starting with expression, isotope-labeling and reconstitution protocols. We review approaches to deal with spectral complexity and limited spectral spectroscopic sensitivity that are usually encountered in NMR-based studies of MPCs. We highlight NMR applications in various classes of MPCs, including G-protein-coupled receptors, ion channels and retinal proteins and extend our discussion to protein-protein complexes that span entire cellular compartments or orchestrate processes such as protein transport across or within membranes. These examples demonstrate the growing potential of NMR-based studies of MPCs to provide critical insight into the energetics of protein-ligand and protein-protein interactions that underlie essential biological functions in cellular membranes.

Insight into the conformational stability of membrane-embedded BamA using a combined solution and solid-state NMR approach

The β-barrel assembly machinery (BAM) is involved in folding and insertion of outer membrane proteins in Gram-negative bacteria, a process that is still poorly understood. With its 790 residues, BamA presents a challenge to current NMR methods. We utilized a “divide and conquer” approach in which we first obtained resonance assignments for BamA’s periplasmic POTRA domains 4 and 5 by solution NMR. Comparison of these assignments to solid-state NMR (ssNMR) data obtained on two BamA constructs including the transmembrane domain and one or two soluble POTRA domains suggested that the fold of POTRA domain 5 critically depends on the interface with POTRA 4. Using specific labeling schemes we furthermore obtained ssNMR resonance assignments for residues in the extracellular loop 6 that is known to be crucial for BamA-mediated substrate folding and insertion. Taken together, our data provide novel insights into the conformational stability of membrane-embedded, non-crystalline BamA.

A structural model for microtubule minus-end recognition and protection by CAMSAP proteins

CAMSAP and Patronin family members regulate microtubule minus-end stability and localization and thus organize noncentrosomal microtubule networks, which are essential for cell division, polarization and differentiation. Here, we found that the CAMSAP C-terminal CKK domain is widely present among eukaryotes and autonomously recognizes microtubule minus ends. Through a combination of structural approaches, we uncovered how mammalian CKK binds between two tubulin dimers at the interprotofilament interface on the outer microtubule surface. In vitro reconstitution assays combined with high-resolution fluorescence microscopy and cryo-electron tomography suggested that CKK preferentially associates with the transition zone between curved protofilaments and the regular microtubule lattice. We propose that minus-end-specific features of the interprotofilament interface at this site serve as the basis for CKKs minus-end preference. The steric clash between microtubule-bound CKK and kinesin motors explains how CKK protects microtubule minus ends against kinesin-13-induced depolymerization and thus controls the stability of free microtubule minus ends.

Magic-Angle-Spinning Solid-State NMR of Membrane Proteins

Solid-state NMR spectroscopy (ssNMR) provides increasing possibilities to examine membrane proteins in different molecular settings, ranging from synthetic bilayers to whole cells. This flexibility often enables ssNMR experiments to be directly correlated with membrane protein function. In this contribution, we discuss experimental aspects of such studies starting with protein expression and labeling, leading to membrane protein isolation or to membrane proteins in a cellular environment. We show that optimized procedures can depend on aspects such as the achieved levels of expression, the stability of the protein during purification or proper refolding. Dealing with native membrane samples, such as isolated cellular membranes, can alleviate or entirely remove such biochemical challenges. Subsequently, we outline ssNMR experiments that involve the use of magic-angle-spinning and can be used to study membrane protein structure and their functional aspects. We pay specific attention to spectroscopic issues such as sensitivity and spectral resolution. The latter aspect can be controlled using a combination of tailored preparation procedures with solid-state NMR experiments that simplify the spectral analysis using specific filtering and correlation methods. Such approaches have already provided access to obtain structural views of membrane proteins and study their function in lipid bilayers. Ongoing developments in sample preparation and NMR methodology, in particular in using hyperpolarization or proton-detection schemes, offer additional opportunities to study membrane proteins close to their cellular function. These considerations suggest a further increase in the potential of using solid-state NMR in the context of prokaryotic or eukaryotic membrane protein systems in the near future.

Suppression of the Aromatic Cycle in Methanol‐to‐Olefins Reaction over ZSM‐5 by Post‐Synthetic Modification Using Calcium

Incorporation of Ca in ZSM‐5 results in a twofold increase of propylene selectivity (53 %), a total light‐olefin selectivity of 90 %, and a nine times longer catalyst lifetime (throughput 792 gMeOH gcatalyst−1) in the methanol‐to‐olefins (MTO) reaction. Analysis of the product distribution and theoretical calculations reveal that post‐synthetic modification with Ca2+ leads to the formation of CaOCaOH+ that strongly weaken the acid strength of the zeolite. As a result, the rate of hydride transfer and oligomerization reactions on these sites is greatly reduced, resulting in the suppression of the aromatic cycle. Our results further highlight the importance of acid strength on product selectivity and zeolite lifetime in MTO chemistry.

Electrophilic aromatic substitution over zeolites generates Wheland-type reaction intermediates

AbstractThe synthesis of many industrial bulk and fine chemicals frequently involves electrophilic aromatic substitution (SEAr) reactions. The most widely practiced example of the SEAr mechanism is the zeolite-catalysed ethylation of benzene, using ethylene as an alkylating agent. However, the current production route towards ethylbenzene is completely dependent on fossil resources, making the recent commercial successes in the zeolite-catalysed benzene ethylation process using bioethanol (instead of ethylene) very encouraging and noteworthy. Unfortunately, there is no information available on the reaction mechanism of this alternative synthesis route. Here, by employing a combination of advanced solid-state NMR spectroscopy and operando UV-Vis diffuse reflectance spectroscopy with on-line mass spectrometry, we have obtained detailed mechanistic insights into the bioethanol-mediated benzene ethylation process through the identification of active surface ethoxy species, surface-adsorbed zeolite–aromatic π-complexes, as well as the more controversial Wheland-type σ-complex. Moreover, we distinguish between rigid and mobile zeolite-trapped organic species, providing further evidence for distinctive host–guest chemistry during catalysis.Bioethanol-based alkylation of benzene is a potentially sustainable route to commodity chemicals, but there is little knowledge of the reaction mechanism. Here, Weckhuysen and co-workers study the zeolite catalysed alkylation of benzene with ethanol, identifying the active alkylating agent and experimentally show the presence of a σ-complex intermediate.