biophysical modeling

This study uses simulations to show that DNA sequence and histone variant identity differentially affect nucleosome structure and histone-DNA interactions in canonical and centromeric nucleosomes.

This study uses molecular dynamics simulations and experiments to show that lipid interactions modulate RhoA conformational dynamics and signaling.

This study shows non-coding RNA disrupts enhancer-promoter interactions when increased, and stabilizes them when decreased, independent of transcription initiation.

The paper identifies BCAS3 as a novel interactor of WIPI2b that regulates its membrane association through interaction with PtdIns3P.

The paper shows that heat stress reverses the growth-promoting thermomorphogenesis pathway in Arabidopsis by suppressing auxin and PIF4 in cotyledons, revealing an active molecular mechanism.

This study identifies distinct peripheral elements in senataxin that mediate R-loop unwinding and RNA polymerase II regulation through structural and biochemical analyses.

This study determines how the I-F3 CRISPR-associated transposase recognizes and pairs transposon ends for transposition using cryo-EM and biochemical analyses.

This paper shows that horizontally acquired mgtC genes can have different physiological roles depending on genomic and biochemical contexts in Salmonella enterica and other bacteria.

This study reveals how PKR's dsRBDs work together to enable selective RNA recognition and activation through a two-step ligand sampling mechanism.

This study shows SF1 helicase Rep translocates processively on ssDNA and, unexpectedly, also on dsDNA, with high speed and processivity, challenging existing models of helicase function.

This study identifies a scaffolding element that drives chromatin rewiring during differentiation by modulating 3D structure and transcription.

This study investigates how the N-terminal regions of CENP-A contribute to the open DNA conformation of centromeric nucleosomes compared to canonical H3 nucleosomes.

The paper identifies a conserved NADase domain, NIR, in bacterial immunity and eukaryotic proteins like human TEP1, linking bacterial defense mechanisms to eukaryotic functions.

The paper shows that protein-driven osmotic pressure regulates nuclear size and function, affecting chromatin organization and gene expression in yeast, human, and fly cells.

This study identifies the structural basis of BRD4 interaction with P-TEFb and shows how BRD4 and AFF4 regulate P-TEFb activity through distinct mechanisms.

This study identifies Myo6's role in DSB repair by interacting with KU70/80 and VCP, facilitated by F-actin, to extract the KU70/80 complex from chromatin.

This study investigates how DNA Ligase IIIα ligates nicks in nucleosomes using biochemical assays, molecular dynamics, and cryo-EM, revealing position-dependent efficiency and structural constraints.

This study reveals how LEAFY transcription factors evolved DNA-binding specificity through structural changes in dimerization mechanisms during the water-to-land transition.

This study shows that DDB2 binding causes different DNA deformations depending on the cyclobutane pyrimidine dimer type, which explains the varying repair rates observed in human cells.

This study examines how mutations in the PWWP domain of DNMT3A affect chromatin recruitment through different mechanisms, leading to distinct disease phenotypes.

This study reveals how HSF1 is regulated by Hsp70 and Hsp90 chaperones through structural and mechanistic analyses, showing Hsp90's role in maintaining HSF1 in a pre-activated state.

This study identifies a multiheme selenoenzyme essential for elemental sulfur respiration in bacteria, revealing its unique catalytic mechanism involving selenium and heme.

This study identifies a conserved interaction between Bim1 and the Ndc80 complex in S. cerevisiae, showing it enhances microtubule attachment strength and is regulated by phosphorylation.

The paper investigates how sustained photoprotection in plants involves enhanced fluorescence intermittency in a subpopulation of LHCII trimers associated with long-lived NPQ.

This study identifies plant-specific and conserved mechanisms by which the PAF1C complex regulates replication stress responses through WEE1-PAF1 interactions and RFC-dependent recruitment.

This study identifies AtMsh1 as a mismatch-directed nuclease in Arabidopsis that facilitates DNA repair in organelles, reducing mutation rates.

This study identifies HMGR as a critical enzyme in B. burgdorferi's mevalonate pathway, revealing its cofactor promiscuity and evolutionary significance.

This study identifies ImuA from Mycolicibacterium smegmatis as a hexameric enzyme with helicase and exonuclease activities essential for DNA damage tolerance during translesion synthesis.