biophysical modeling

The paper surveys histone diversity in archaea using bioinformatics and simulations, identifying five histone types and their genomic strategies.

The paper identifies a novel small RNA, ASpks2, in Mycobacterium tuberculosis that promotes bacterial survival in macrophages by targeting polyketide synthase 2.

This study investigates the structural and functional properties of BrxC, a conserved AAA+ ATPase in the BREX phage restriction system, revealing its role in mediating competing protein associations and DNA binding that regulate host methylation and phage restriction.

The paper determines the structural basis of substrate recognition by PafA, showing that broad specificity arises from dynamic, geometrically compatible interactions rather than sequence-specific binding.

This paper develops a nonlinear biomechanical model to explain varying outcomes in clavicle fractures by analyzing stability and bifurcation mechanisms.

This paper defines the molecular basis for TCR peptide recognition by the CIA targeting complex using binding measurements, bioinformatics, and structural modeling, revealing a hierarchy of physicochemical determinants.

The paper identifies AMI-1 as an inhibitor of NMNAT1, shows its effect on NAD+ levels and cancer cell viability, and determines its binding mechanism via cryo-EM.

The paper develops a biophysical model of phagocytic cup dynamics that incorporates membrane tension, showing it leads to slower engulfment and stalled engulfment, with implications for immune function and drug delivery.

This study uses ancestral protein reconstruction to uncover the molecular mechanism of substrate specificity in FN3K and KT3K enzymes, revealing an allosteric network that modulates substrate recognition.

This study identifies a novel mechanism where Gq/11 and G12/13 activation causes SH2 domain-containing proteins to translocate from the plasma membrane to the nucleus, reducing RTK signaling activity.

The paper shows that mitochondrial DNA nucleoid distribution is controlled by pearling and cristae structure, revealing a mechanism for nucleoid spacing and segregation.

This study identifies Rab5 as an interacting partner of the L. pneumophila effector VipA, showing that Rab5 binding inhibits VipA's ability to promote actin polymerization.

This study identifies XPC as essential for protecting Th17 cells from oxidative DNA damage, showing its role in DNA repair, differentiation, and function.

This study investigates how DNA supercoiling affects Cas9 off-target cleavage by mapping cleavage rates and sites across different topologies using NucleaSeq and a biophysical model.

This study quantifies the binding affinities of TRPM2 domains for ADPR analogs and shows that MHR1/2 drives activation while NUDT9H maintains structural integrity.

This study investigates the structural and dynamic basis of non-canonical recognition between SF3A1 ULD and U1 snRNA SL4 during spliceosome assembly, revealing dual recognition mechanisms and the impact of mutations on protein-RNA interactions.

The paper identifies Bacillus toyonensis biovar Thuringiensis as a potential entomopathogen capable of producing insecticidal crystals, challenging previous classifications of related strains.

This paper identifies a host-encoded toggle switch involving NOD2 and GIV that controls cAMP levels in macrophages, converting tolerant cells into microbicidal machines to restore microbial clearance and gut barrier integrity.

This study reveals how TRiC folds the large ciliary protein IFT172 using a non-canonical open-state mechanism involving Z-shaped bending and fold-and-eject dynamics.

This study investigates GlmR's role in carbon regulation, cell morphology, and stress response in Bacillus subtilis, revealing its post-translational regulation and enzymatic function.

This study investigates the structural and biochemical properties of Csx15, a ring nuclease that binds cyclic nucleotides and regulates antiviral defense by modulating cOA levels.

This study identifies how eLOTUS domains activate Vasa by promoting its RNA and ATP binding through a charged disordered sequence, revealing a localization-dependent regulatory mechanism.

This study investigates how uridylation mediates RNA decay in Drosophila by showing how Tailor generates oligo(U) intermediates and how Dis3l2 decodes these to initiate decay.

This study identifies a molecular switch in NAC that prevents mitochondrial protein mistargeting by SRP, showing that mutations disrupt this mechanism and cause ER stress.

This study investigates the ISG15-USP18-STAT2 inhibitory complex's structure and function using AlphaFold and biochemical methods, revealing critical residues and patient mutations affecting its interaction.

The paper identifies a conformational switch in eIF5 that regulates translation initiation at AUG and non-AUG codons by stabilizing or destabilizing the initiation complex.

This study uses simulations to show that hydration dynamics enable proton transport in Complex I by aligning with excess protons, revealing a coupling between water and proton movement.

The paper reassesses the historical record of Pionus fuscus in Colombia using multiple lines of evidence, concluding it does not occur there.

This study identifies two novel T6SS effectors in C. jejuni and shows their role in bacterial antagonism and host cell interaction.

The paper characterizes structural, biophysical, and virological properties of HIV-1 capsid-targeting antivirals, showing improved potency and stability through chemical modifications of PF74.