FEBS Letters

doi: 10.1002/1873-3468.14658pmid: N/A

Wright, Duncan E.

doi: 10.1002/1873-3468.15018pmid: 39279609

Although publication in scholarly peer‐reviewed journals remains the gold standard for communication of findings in the life sciences, the gold has been debased in the digital age by various impurities, including (a) reviewer fatigue, (b) fraud, paper mills, and the perils of artificial intelligence, (c) predatory journals, (d) the ongoing use of journal impact factor as a proxy for individual article quality, and (e) salami‐slicing and other unethical practices. In this article, I present a detailed overview of these problems, as well as solutions proposed and implemented to counter them. Finally, I suggest that these are all symptomatic of a wider problem, namely the culture of ‘publish or perish’ and ongoing issues with how researcher performance is evaluated for grant, hiring, and promotion decisions. Only by working towards a global shift in the way scientists view the purpose of publication can we finally remove the impurities and refine the gold.

Fox, Daniel R.; Samuels, Imogen; Binks, Sebastian; Grinter, Rhys

doi: 10.1002/1873-3468.14958pmid: 38880764

Haemoglobin (Hb) is a vital oxygen carrier in vertebrates. Low blood Hb levels may indicate anaemia or genetic disorders, while its presence in the lower digestive system suggests colon cancer. Detecting and quantifying human Hb is essential for medical diagnostics. A nanobody‐based sandwich‐ELISA test was recently developed utilising llama‐derived nanobodies NbE11 and NbB9. These nanobodies specifically bind to human Hb without cross‐reacting with Hb from other vertebrates. Here, we determine the crystal structure of NbE11 in complex with human Hb. NbE11 binds Hb with high affinity, predominantly binding the β‐Hb subunit. Structural differences between human Hb and other vertebrates at the NbE11 binding interface likely explain the assay's lack of cross‐reactivity, providing insights for developing Hb binding diagnostics.

Sorada, Tomoki; Walinda, Erik; Morimoto, Daichi

doi: 10.1002/1873-3468.14951pmid: 38853439

Lys48‐linked ubiquitin chains, regulating proteasomal protein degradation, are known to include cyclized forms. This cyclization hinders recognition by many downstream proteins by occluding the Ile44‐centered patch. In contrast, the A20‐like Znf domain of ZNF216 (a ubiquitin‐binding protein, A20 Znf) is expected to bind to cyclic ubiquitin chains via constitutively solvent‐exposed surfaces. However, the underlying interaction mechanism remains unclear. Here, our ITC and NMR experiments collectively showed that cyclization did not interfere with and even slightly enhance the molecular recognition of diubiquitin by A20 Znf. This effect is explained by the cyclization‐induced repression of conformational dynamics in diubiquitin and an enlarged molecular interface in the complex. Thus, these results suggest that cyclic ubiquitin chains can be involved in regulation of ZNF216‐dependent proteasomal protein degradation.

Satoh, Tadashi; Yagi‐Utsumi, Maho; Ishii, Nozomi; Mizushima, Tsunehiro; Yagi, Hirokazu; Kato, Ryuichi; Tachida, Yuriko; Tateno, Hiroaki; Matsuo, Ichiro; Kato, Koichi; Suzuki, Tadashi; Yoshida, Yukiko

doi: 10.1002/1873-3468.15003

Yokoyama, Takeshi; Takayama, Yuki; Mizuguchi, Mineyuki; Nabeshima, Yuko; Kusaka, Katsuhiro

doi: 10.1002/1873-3468.14961pmid: 39031546

SIRT5, one of the mammalian sirtuins, specifically recognizes succinyl‐lysine residues on proteins and catalyzes the desuccinylation reaction. In this study, we characterized SIRT5 mutants with hydrophobic amino acid substitutions at Q140 and N141, in addition to the catalytic residue H158, known as an active site residue, by the Michaelis–Menten analysis and X‐ray crystallography. Kinetic analysis showed that the catalytic efficiency (kcat/Km) of the Q140L and N141V mutants decreased to 0.02 times and 0.0038 times that of the wild‐type SIRT5, respectively, with the activity of the N141V mutant becoming comparable to that of the H158M mutant. Our findings indicate that N141 contributes significantly to the desuccinylation reaction.

Tamarín, Stephanie; Galaz‐Davison, Pablo; Ramírez‐Sarmiento, César A.; Babul, Jorge; Medina, Exequiel

doi: 10.1002/1873-3468.14972pmid: 38946055

The human FoxP transcription factors dimerize via three‐dimensional domain swapping, a unique feature among the human Fox family, as result of evolutionary sequence adaptations in the forkhead domain. This is the case for the conserved glycine and proline residues in the wing 1 region, which are absent in FoxP proteins but present in most of the Fox family. In this work, we engineered both glycine (G) and proline–glycine (PG) insertion mutants to evaluate the deletion events in FoxP proteins in their dimerization, stability, flexibility, and DNA‐binding ability. We show that the PG insertion only increases protein stability, whereas the single glycine insertion decreases the association rate and protein stability and promotes affinity to the DNA ligand.

Inobe, Tomonao; Sakaguchi, Runa; Obita, Takayuki; Mukaiyama, Atushi; Koike, Seiichi; Yokoyama, Takeshi; Mizuguchi, Mineyuki; Akiyama, Shuji

doi: 10.1002/1873-3468.14986pmid: 39031920

Inducible dimerization systems, such as rapamycin‐induced dimerization of FK506 binding protein (FKBP) and FKBP–rapamycin binding (FRB) domain, are widely employed chemical biology tools to manipulate cellular functions. We previously advanced an inducible dimerization system into an inducible oligomerization system by developing a bivalent fusion protein, FRB–FKBP, which forms large oligomers upon rapamycin addition and can be used to manipulate cells. However, the oligomeric structure of FRB–FKBP remains unclear. Here, we report that FRB–FKBP forms a rotationally symmetric trimer in crystals, but a larger oligomer in solution, primarily tetramers and pentamers, which maintain similar inter‐subunit contacts as in the crystal trimer. These findings expand the applications of the FRB–FKBP oligomerization system in diverse biological events.

Koopmeiners, Simon; Gilzer, Dominic; Widmann, Christiane; Berelsmann, Nils; Sproß, Jens; Niemann, Hartmut H.; Fischer von Mollard, Gabriele

doi: 10.1002/1873-3468.15002pmid: 39152524

l‐Amino acid oxidases (LAAOs) catalyze the oxidative deamination of l‐amino acids to α‐keto acids. Recombinant production of LAAOs with broad substrate spectrum remains a formidable challenge. We previously achieved this for the highly active and thermostable LAAO4 of Hebeloma cylindrosporum (HcLAAO4). Here, we crystallized a proteolytically truncated surface entropy reduction variant of HcLAAO4 and solved its structure in substrate‐free form and in complex with diverse substrates. The ability to support the aliphatic portion of a substrate's side chain by an overall hydrophobic active site is responsible for the broad substrate spectrum of HcLAAO4, including l‐amino acids with big aromatic, acidic and basic side chains. Based on the structural findings, we generated an E288H variant with increased activity toward pharmaceutical building blocks of high interest.