protein folding & dynamics

This study uses molecular dynamics simulations to show how the G93A mutation in SOD1 increases electrostatic loop fluctuations, while the I35S mutation reduces these fluctuations, linking structural changes to aggregation in fALS.

This paper designs de novo ligases that achieve site-specific ubiquitylation of a target protein with high selectivity and efficiency.

The paper develops a computational model to show that Hsp70 chaperones only delay, not prevent, protein aggregation, depending on client-specific kinetic and thermodynamic properties.

This paper introduces HV-MultiScaleGNN, a graph neural network framework for predicting host-virus protein-protein interactions using network topology, achieving strong performance across multiple evaluation metrics.

This study investigates how ADP and magnesium influence the structural changes and higher-order assembly of peroxiredoxin 2, showing distinct roles in disassembly and reassembly processes.

This study identifies a phosphorylation-dependent conformational change in the K19 head domain that affects filament assembly and interactions with GSK3β, but not 14-3-3 proteins.

This paper introduces Cadense, a machine learning framework that generates antibody conformational ensembles from sequence, capturing dynamic properties and improving docking accuracy.

The paper analyzes six-residue Omega-loops in protein complexes, showing their structural constraints, sequence conservation patterns, and functional significance through sequence design and mutation mapping.

This study uses nonequilibrium molecular dynamics to show frequency-dependent structural changes in amyloid fibrils under terahertz pulses, identifying two electric-field thresholds for disruption.

This study shows that AlphaFold2 distance maps can reveal multi-state protein structures, enabling prediction of alternative conformations with high accuracy.

This study characterizes the conformational dynamics and phosphorylation-dependent changes in the SF3B1 N-terminal domain using a combination of biophysical and computational methods.

This study shows that bL9 prevents recoding events in collided ribosomes by stabilizing their interaction and reducing frameshifting and hopping.

The paper develops a biosensor platform using monomeric streptavidin to evaluate binding domains for small molecules and proteins, demonstrating ligand-dependent activation with biotinylated targets.

This study provides direct evidence of transient binding between α-synuclein C-terminus and synaptobrevin-2 using NMR and other biophysical methods, suggesting a role in neuronal exocytosis.

The paper uses AI to model 109,282 human protein interactions, maps pathogenic variants to these structures, and identifies interface mutations in disease contexts.

This paper introduces ipSAE, a directional scoring framework for assessing confidence in predicted biomolecular complexes, showing improved performance over existing methods in protein-ligand and protein-DNA interactions.

This study shows that selenocysteine (Sec) plays a role in protein folding during biosynthesis, not just in mature proteins, by demonstrating that its incorporation affects dimer formation in SELENOM.

The paper evaluates how natural genetic diversity affects the thermodynamic impact of pathogenic variants in small human proteins, showing significant background-dependent stability changes in most tested variants.

This study shows the ER membrane protein complex (EMC) acts as a chaperone to facilitate the assembly of voltage-gated calcium channels during their biogenesis.

This study validates engineered hyper-stable human serum albumin variants for their structural integrity and functional adaptability in biotechnological applications.

This paper introduces a series of BzAM terpolymers with varying hydrophobicity to solubilize GPCRs in nanodiscs, showing that solubilization efficiency and functional integrity are preserved.

HTFAST enables high-throughput, quantitative affinity measurement of cell-free expressed binders using FRET, validated with nanobodies and SARS-CoV-2 sdAbs.

The paper introduces FlexENN, a graph neural network that predicts binding energies for both folded and intrinsically disordered protein complexes, showing improved performance over rigid-body methods.

The paper predicts the structure of a 89-kDa invasion-tip protein from Holospora obtusa and suggests a pH-dependent conformational change may aid in escaping the host digestive vacuole.

This paper determines two X-ray crystal structures of a thermophilic lipase, showing that Pro367 ring puckering is associated with calcium binding and conformational selection.

The paper uses high-resolution NMR spectroscopy to study protein interactions and modifications within intact mitochondria, providing insights into mitochondrial protein function and stability.

The paper investigates how the highly acidic SH3 domain binds to an intrinsically disordered partner through an encounter complex intermediate, revealing the role of long-range electrostatic interactions.

The paper determines the structure of the cysteine-rich domain of SEP15 using AlphaFold and NMR, revealing a novel helical fold stabilized by disulfide bonds.

This study identifies how PIP3 activates an ancestral Tec kinase by displacing its PH domain from an inhibitory interaction with its kinase domain.

This study identifies PAD1-4 citrullination sites in histone tails using NMR spectroscopy, revealing differential specificity and conformational effects in nucleosomes.