mechanistic / dynamical model

The paper uses molecular dynamics simulations to identify a unifying mechanism for excipient-mediated protein thermal stability based on shape complementarity between proteins and solvents.

This study investigates the membrane-dependent structure of CPXV012 and its interaction with TAP, revealing a two-helical organization and flexible ER-luminal region critical for TAP recognition.

This study models CISH-KO TIL therapy in gastrointestinal cancer, finding that T-cell persistence and endogenous competition are key determinants of treatment response.

This study shows that glassy dynamics in epithelial tissues arise from mechanochemical feedback and crowding, not just crowding alone.

The paper compares aromatic ring flip kinetics in GB1 protein across crystals, IgG complexes, and solution, showing reduced flipping in crystals and revealing how crystal environments restrain motion.

This study shows cohesin accelerates homology search in HR repair by transforming 3D diffusion into 1D scanning through loop extrusion and cohesion.

This study identifies the molecular mechanism by which the plant immune receptor LORE binds and responds to 3-hydroxy fatty acid ligands through a dynamic loop in its G-type lectin domain.

This study uses molecular dynamics simulations to compare unfolding mechanics of 51 keratin proteins, revealing rate-dependent nanomechanical responses and correlations with molecular descriptors.

This paper introduces the murburn model, which explains bacterial motility through metabolic water ejection, showing it can reproduce observed swimming speeds and rotation without a rotary motor.

This study uses molecular dynamics simulations to investigate how static magnetic fields affect the CNGC6 ion channel and lipid organization in tomato cells, finding structural changes in the channel but not in the lipid bilayer.

This study examines how pH changes affect the biophysical properties of YghA from E. coli, revealing structural instability at acidic pH and altered interactions with NADH.

This paper identifies residue W230 as a dynamic gate in b0,+AT that regulates arginine transport through side chain flipping, using molecular dynamics simulations.

This study investigates the role of an N-terminal amphipathic helix in Nramp transporters, showing it regulates conformational dynamics and metal ion transport.

The paper models and validates the coordination mechanism between PilT and PilU ATPases during type IV pilus retraction using AlphaFold 3 and molecular dynamics simulations.

The paper studies how sperm navigate near walls in flowing fluids, identifying a new oscillation state and a hydrodynamic buffer zone that stabilizes surface navigation.

The paper uses molecular dynamics simulations to show how Aspein, an acidic protein from pearl oysters, controls calcium carbonate polymorphism by sequestering Ca2+ and stabilizing calcite over aragonite.

The paper investigates organ-specific fibroblast dynamics in cardiac and pulmonary fibrosis using experimental and computational methods, revealing differences in collagen matrix organization and motility behavior.

This study uses molecular dynamics simulations to investigate how the intrinsically disordered regions of FUS recognize U1 snRNA, revealing distinct interaction mechanisms and structural changes upon RNA binding.

This paper identifies specific interfacial residues in IGPS that modulate allosteric regulation through structural and dynamic changes induced by targeted mutations.

This study investigates how deletion of the central region of PrP affects its structure and dynamics, revealing altered conformational behavior and membrane interactions linked to neurotoxicity.

This study identifies four recurrent dengue envelope protein interaction architectures using computational methods and suggests viral stability depends on local network context.

This study investigates how anionic and cationic surfactants affect the conformational stability of a cationic protein using molecular dynamics simulations.

This study models the structure of LRP1 using homology and neural network-based methods, revealing glycan-mediated dimerization and its role in stabilizing the protein's quaternary structure.

Across 12 µs of all-atom simulations, cholesterol stabilizes the sigma-1 receptor trimer, while haloperidol, unlike (+)-pentazocine, engages β6-strand W136 to tighten interprotomer coupling.

This paper uses pressure and temperature to study how TMV coat protein assembly changes, revealing localized structural dynamics and epitope masking under high pressure.

The paper reports a spontaneous structural transition in the insulin receptor during molecular dynamics simulation, revealing a conformation compatible with hybrid insulin binding sites.

This study uses molecular dynamics simulations to show that antibody maturation increases rigidity in protein-contacting regions and flexibility at glycan interfaces.

The paper develops a deformation gradient tensor model to describe the roll-spiral transformation in protein refractile bodies, linking macroscopic morphology with microscopic lattice deformation.

The paper demonstrates that bacterial flagellar torque has two components driving spin and precession, supported by bead assay experiments and a mechanical model.