Biology subjects

Barends, T. R. M.

Publications and source records attributed to Barends, T. R. M..

6 recordsLinked to original sources

bioRxiv2026

An Unprecedented Cluster in a Methanotroph Acetol Dehydrogenase

Biocatalytic metal-containing clusters are nanometer-sized chemical reactors that enable enzymes to perform chemistry far beyond what would be possible with amino acids alone 1,2. These clusters display a remarkable variability3 and elucidating their exact mechanisms is often difficult to determine, requiring input from a multitude of techniques ranging from spectroscopic to structural and theoretical methods. Thus, for unknown clusters, it is essential to accumulate, collate, and interpret as much information as possible from every relevant technique available. Here we report the discovery and in-depth, interdisciplinary characterization of an entirely novel, [Cu-4Fe-4S] cluster in the protein acetol dehydrogenase (AceDH). AceDH, isolated directly from Methylacidiphilum fumariolicum SolV cells, catalyzed the oxidation of acetol to methylglyoxal, proving its role in the 2-propanol/acetone metabolism of methanotrophs4-6. Structural, spectroscopic and electrochemical analyses reveal the [Cu-4Fe-4S] cluster has a unique three-dimensional- and electronic structure involving electronic coupling between the copper and one of the iron atoms, likely contributing to its high, +275 mV, redox potential. The binding site for the novel cluster is composed of two protein subunits and involves a novel motif. These findings expand the known repertoire of biological metal cofactors and provide insight into how heterometallic clusters are adapted for biological processes.

biochemistry↗

bioRxiv2026

β-Ketoacyl Synthase II Homologs from a Ladderane-Producing Organism Form a Ketosynthase/Chain Length Factor-like functional heterodimer

Ladderanes are extraordinary, highly strained chemical structures consisting of linearly concatenated cyclobutane rings. Ladderane-containing fatty acids are found in the lipids of anaerobic ammonium oxidizing (anammox) bacteria, reducing the proton permeability of their membranes to support their unique metabolism. Almost nothing is known about the biosynthesis of ladderanes, but a gene cluster unique to ladderane-producing bacteria is likely to be involved. This cluster encodes radical SAM enzymes as well as homologs of enzymes known from fatty acid biosynthesis. Amongst these are two homologs of FabF, the enzyme performing chain elongation in canonical fatty acid synthesis. The presence of two chain-elongating enzymes is unexpected; a single one would be expected to suffice, and the fact that one of the two homologs has a mutated, nonfunctional catalytic triad deepens the mystery. Here we present an in-depth characterization of the FabF homologs from anammox organisms, using biochemistry, enzymology, structural biology and computational biology. We show that the two homologs form a heterodimer analogous to the ketosynthase/chain length factor complexes known from polyketide synthases. This heterodimer is capable of performing the decarboxylation of malonate-loaded acyl carrier protein, thus initiating fatty acid biosynthesis. The crystal structure of the heterodimer explains how homodimer formation is avoided, and shows the details of the substrate binding tunnel. Mechanism-based crosslinking studies of wild-type and mutant heterodimers show the influence of residues on both subunits on substrate preference (which differs from canonical FabFs), and, together with computational studies, the crystal structure of the heterodimer in complex with substrate-loaded ACP helps explain its preference for ladderane-specific ACP. The results clearly refute an early proposal for a ladderane biosynthetic mechanism and greatly expand our current knowledge on how anammox bacteria produce their extraordinary lipids.

biochemistry↗

bioRxiv2025

Rieske Iron-Sulfur Cluster Proteins from an Anaerobic Ammonium Oxidizer Suggest Unusual Energetics in their Parent Rieske/cytochrome b complexes

Anaerobic ammonium-oxidizing (anammox) bacteria employ a unique, hydrazine-based pathway to obtain energy from nitrite and ammonium. These organisms express distinct Rieske/ cytochrome b complexes whose precise role in anammox metabolism remains unclear, but which has been proposed to include the generation of NAD(P)H. This would require energetics and structural features unusual for such complexes. Here we present crystal structures and electrochemical investigations of the Rieske subunits of two of these complexes from the anammox organism Kuenenia stuttgartiensis, Kuste4569 and Kustd1480. Both proteins display high redox potentials (>+300 mV), which can be in part explained by their crystal structures and which fit perfectly into the energetic scheme of the proposed NAD(P)H generation mechanism. Moreover, AlphaFold3 models of the parent complexes trace out a path for the electrons required for NAD(P) production, which includes a proposed, novel b-type heme in the membrane-bound part of the complex.

biochemistry↗

bioRxiv2022

Influence of pump laser fluence on ultrafast structural changes in myoglobin

High-intensity femtosecond pulses from an X-ray free-electron laser enable pump probe experiments for investigating electronic and nuclear changes during light-induced reactions. On time scales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer1. However, all ultra-fast TR-SFX studies to date have employed such high pump laser energies that several photons were nominally absorbed per chromophore2-14. As multiphoton absorption may force the protein response into nonphysiological pathways, it is of great concern15 whether this experimental approach16 allows valid inferences to be drawn vis-a-vis biologically relevant single-photon-induced reactions17. Here we describe ultrafast pump-probe SFX experiments on photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe-CO bond distance (predicted by recent quantum wavepacket dynamics15) are seen to depend strongly on pump laser energy. Our results confirm both the feasibility and necessity of performing TR-SFX pump probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing design and interpretation of ultrafast TR-SFX pump probe experiments16 such that biologically relevant insight emerges.

biophysics↗

bioRxiv2022

Xtrapol8: automatic elucidation of low-occupancy intermediate-states in crystallographic studies

Unstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, hindering structure determination by conventional methods. To automatically extract such structures, we developed Xtrapol8, a program which (i) applies various flavors of Bayesian-statistics weighting to generate the most informative Fourier difference maps; (ii) determines the occupancy of the intermediate states by use of hitherto unavailable methods; (iii) calculates various types of extrapolated structure factors while handling the issue of negative structure factor amplitudes, and (iv) refines the corresponding structures.

biophysics↗

bioRxiv2021

Rational control of structural off-state heterogeneity in a photoswitchable fluorescent protein provides switching contrast enhancement

Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, a key parameter that largely dictates the achievable resolution in nanoscopy applications, and chromophore conformation in the non-fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off-state conformations, trans1 and trans2, located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off-state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high-level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue- and red-shifts of the absorption bands associated to trans1 and trans2, respectively. Thus, due to elimination of trans2, the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two-fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2-V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.

biophysics↗