Current Opinion in Structural Biology

The ultimate mission of de novo enzyme design methodology is to develop strategies that produce new-to-nature enzymes that match the efficiency and versatility of natural ones. Until recent years, design methods yielded enzymes with low catalytic efficiencies even for simple reactions, underscoring the need for tighter control over backbone structure and active-site preorganization. Two approache…

Amyloid fibrils are involved in devastating conditions such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and systemic amyloidosis. They exhibit polymorphism, meaning that a single protein sequence can adopt different amyloid folds that vary with time and self-assembly conditions. Polymorphism confounds structure-based drug design and raises fundamental questions regarding wh…

G-protein-coupled receptors (GPCRs) are a large family of membrane proteins that mediate cellular responses to diverse stimuli and serve as targets for ∼35 % of Food and Drug Administration-approved drugs. Their structural complexity, conformational heterogeneity, and membrane embedding have historically hindered experimental characterization, although advances in crystallization and cryogenic el…

Membrane proteins (MPs) play essential roles in a wide range of cellular processes and represent major therapeutic targets. Nevertheless, their structural and functional characterization remains challenging due to inherent difficulties in production, extraction, and stabilization outside their native lipid environment. The rise of cryogenic electron microscopy (cryo-EM) has markedly accelerated t…

Single-molecule experiments have become an integral part of modern structural biology. Unlike other methods, single-molecule Förster resonance energy transfer (smFRET) spectroscopy opens direct access to distance-based temporal trajectories of protein motions. Recent innovations in analysing smFRET experiments with correlation and photon-trajectory based methods have pushed the time resolution of…

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are critical regulators in health and disease but remain underexploited as drug targets. Unlike folded proteins, they populate dynamic ensembles where interactions can be transient or multivalent, and both enthalpic and entropic contributions shape binding, complicating ligand discovery. Here, we analyze three ke…

Chemical cross-linking coupled with mass spectrometry (XL-MS) has become a powerful tool for probing residue-level proximities within macromolecular assemblies. By providing sparse but informative distance restraints, XL-MS can be integrated with electron microscopy and domain-level high-resolution structures to model the architecture of protein complexes. Unlike X-ray crystallography, electron m…

New deep learning-based methods for modeling and generation of protein structures have opened a new chapter in the field of protein design, transforming many previously unattainable challenges into routine tasks. Protein-binder design, an important and challenging task in protein engineering, has also experienced significant progress, promising to provide solutions to many therapeutic and bioengi…

Nearly a quarter of the proteins encoded in most organisms are transmembrane proteins. Contrary to textbook description, many feature a hydrophilic groove which is laterally exposed to the hydrophobic region of the lipid membrane. This cavity is stabilized by neighboring lipid headgroups that sink deep into the membrane and consequently move bidirectionally from one leaflet to the other, in a pro…