mechanistic / dynamical model

This paper shows antibiotic condensates activate magnesium signaling to enhance bacterial survival and drug tolerance.

This study investigates how temperature affects tryptophan fluorescence in proteins by analyzing rotamer population shifts in bovine serum albumin using molecular dynamics and quantum mechanical methods.

This study uses molecular dynamics simulations to show how oligomannose Fc glycans alter CD16a binding by changing energetic interactions and conformational dynamics.

This study uses molecular dynamics simulations to investigate how HIV-1 Env proteins reorganize during viral maturation, revealing clustering mechanisms and implications for antibody accessibility.

This study uses molecular simulations to reveal how lipid nanoparticles escape endosomes, identifying key factors like lipid shape and pH sensitivity that influence their efficiency.

The paper shows that cytoplasm in early embryos behaves as a locally switchable active material, enabling long-range transport of components during cleavage.

This study investigates the emergence of two key cofactor-binding protein folds by analyzing their metabolic roles, structural organization, and folding mechanisms.

This study shows lipid nanoparticles form protein coronas through lipoprotein fusion, not surface adsorption, using cryo-EM and simulations.

The paper identifies small-molecule and peptide inhibitors of NDST1 as potential substrate-reduction therapies for MPS IIIC using computational screening and molecular dynamics.

The paper links SAC silencing with mitotic memory through microtubule occupancy at kinetochores, showing that high occupancy enables timely silencing and prevents mitotic stopwatch-induced proliferation block.

ContiDesigner is a tool for designing continuous fermentation cascades that identifies optimal operating conditions to maximize productivity.

This study uses molecular dynamics simulations to show that longer amylose oligomers are more stable in hot water than shorter ones, with structural collapse observed in shorter chains.

This study uses molecular dynamics simulations to compare the effects of N-glycosylation on IgG2 and IgG4 antibodies, showing subclass-dependent impacts on flexibility and antigen binding.

The paper develops a reduced mechanobiological framework linking hemodynamic shear to mechanosensitive calcium entry in platelets, identifying a conditioning-test protocol to distinguish memory effects from other priming mechanisms.

This paper develops a multiscale computational model of pulmonary vascular remodeling in PH, showing it can predict pressure, wall thickness, and stiffness changes in response to treatment.

The paper defines the MxA-Thogotovirus nucleoprotein interface using structural modeling and experimental validation, revealing key residues involved in restriction and escape.

This study shows molecular asymmetry and sequence architecture encode electric potential profiles in biomolecular condensates, revealing how charge distribution and protein structure influence interfacial potentials.

This study investigates how PTMs modulate peptide translocation through graphene nanopores using molecular dynamics, finding that acetylation and phosphorylation significantly alter dwell-time statistics and current blockade.

This study investigates allosteric signal communication in AChRs, showing distinct activation pathways in liganded vs unliganded states and identifying a continuous allosteric network.

This study uses molecular dynamics simulations to show that spacer heterogeneity in stickers-and-spacers polymers promotes condensation but reduces condensate organization and compositional robustness.

The paper shows that Erv14/cornichon receptor dynamics and bilayer thickness influence directional ER-Golgi traffic through a mechanism called HEIST.

This study identifies the flexible N-terminal domain of Sorcin as a critical regulator that enhances Ca2+ responsiveness by stabilizing its active conformation through dynamic contacts.

This study identifies a stress-lipid kinase axis in NEPC driven by PIKfyve, revealing a synthetic vulnerability between PIKfyve and FASN that can be exploited for therapeutic targeting.

This paper uses molecular dynamics simulations to show that the transmembrane domain (TMD) of SARS-CoV-2 spike regulates the kinetics of S2 conformational transitions by modulating TMD dynamics and coupling with S1.

This study investigates how functionalized graphene quantum dots (GQDs) bind to Tau fibrils in Alzheimer's disease, identifying binding sites and showing that anionic GQDs preferentially bind to specific regions, potentially aiding in TA disaggregation.

The paper shows that backbone hydrogen bonding determines condensate material states, as demonstrated by experiments with tetrapeptides and simulations.

This study identifies an O-GlcNAc modification on PKM2 that promotes PDAC progression through the ARNT-CDC27-AKT pathway by enhancing aerobic glycolysis.

This paper uses molecular dynamics simulations of AAA+ unfoldases to show structural asymmetry and allosteric networks generate kinetic asymmetry, enabling directional substrate translocation despite stochastic ATP hydrolysis.

This study identifies HSD11B1 as a direct target of magnesium isoglycyrrhizinate, revealing its therapeutic mechanism in alcohol-associated liver disease through the HSD11B1-SREBP2-IDI1 signaling axis.

This study investigates how phosphorylation affects the structure and function of motif A in SIRT1, showing that phosphomimetic mutation at Ser27 enhances SIRT1 activity and induces structural ordering of the disordered region.