Molecular modelling articles from across Nature Portfolio

Cryo-electron microscopy of brain tissue from two individuals with Down syndrome showed amyloid-β (Aβ) and tau filaments identical to those found in individuals with sporadic or dominantly inherited Alzheimer disease (AD), but also two types of Aβ₄₀ filaments with distinct structures different from those previously reported in AD and cerebral amyloid angiopathy.

The molecular heterogeneity of glycosylated biotherapeutics often complicates analysis by intact mass spectrometry. Here, the authors propose a simplified procedure for characterization that employs proton transfer charge reduction. Integration with glycomic and glycopeptide datasets can further provide glycoform-level information.

Understanding the stability and activity of freeze-dried bio-macromolecules at low degrees of hydration is crucial for pharmaceutical and food industries, however, the building of in silico models for dynamical studies at a molecular level needs careful consideration. Here, the authors propose a modelling protocol that mimics experimental protein lyophilization, and proteins in weakly hydrated amorphous states, and validate it against experimental neutron scattering data.

Gloeobacter proton-gated ion channel (GLIC) is a convenient model of pentameric ligand-gated ion channels. Here, Bharambe & Li et al. report structures and simulations of GLIC with insights into the role of lipids in GLIC gating mechanism.

Recent combinations of structure-based and sequence-based calculations and machine learning tools have dramatically improved protein engineering and design. Although designing complex protein structures remains challenging, these methods have enabled the design of therapeutically relevant activities, including vaccine antigens, antivirals and drug-delivery nano-vehicles.

It is hard to correlate force, torque and localization information. The authors report Combined Optical and Magnetic BIomolecule TWEEZers, COMBI-Tweez, that integrates optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy: they demonstrate visualisation of higher order structural motifs in DNA.

Cryo-electron microscopy of brain tissue from two individuals with Down syndrome showed amyloid-β (Aβ) and tau filaments identical to those found in individuals with sporadic or dominantly inherited Alzheimer disease (AD), but also two types of Aβ₄₀ filaments with distinct structures different from those previously reported in AD and cerebral amyloid angiopathy.

New work shows that in mammals, the iDDR motif of telomere factor TRF2 inhibits the MRE11–RAD50–NBS1 (MRN) complex at chromosome ends through a direct iDDR–RAD50 interaction. Unrelated protein motifs in yeasts inhibit MRN functions via an analogous mechanism, suggesting a convergent evolution in eukaryotes to control MRN action at telomeres.