structural biology

This study reveals how cyclic tetra-adenylate binds to Cap1, inducing conformational changes that open a membrane pore and cause depolarization during the type III CRISPR immune response.

The paper challenges the hypothesis that the yjdF riboswitch is regulated by azaaromatic compounds by showing it binds multiple ligands similarly but requires conserved nucleotides for activation.

The paper evaluates a structure-based drug discovery pipeline for targeting MALAT1 using 21 ligands, identifying a binding mode that aligns with experimental affinity trends.

This study investigates how GroEL/ES interacts with nascent proteins on ribosomes, showing that GroEL binds and destabilizes substrates, while GroES facilitates partial encapsulation and refolding.

This study investigates K+ transport through the inter-subunit tunnel of KdpFABC using simulations and experiments, finding that the tunnel is mostly water-filled with a single K+ binding site and a high energy barrier.

This study identifies gallic acid as an inhibitor of PaSuhB, revealing its role in suppressing bacterial growth and motility through structural and functional analysis.

The paper presents crystal structures and electrochemical data on Rieske subunits from anammox bacteria, supporting a novel NAD(P)H generation mechanism with unusual redox potentials and structural features.

This study characterizes LIG1's structural and biochemical interactions with oxidatively damaged DNA during the final steps of base excision repair.

This study identifies ERC1 as a protein that forms biomolecular condensates to recruit ATG8 and NBR1, promoting autophagosome formation and enhancing heat tolerance in Arabidopsis.

This study shows that overglycosylation of collagen type I affects fibril structure by altering local packing and sub-band displacements without changing overall periodicity.

This paper uses machine learning to identify allosteric networks in Cas9, revealing key residues and an electrostatic valley that stabilize its structure and specificity.

This study identifies Adig as a regulator of lipid droplet formation by stabilizing the dodecameric seipin complex, leading to increased fat mass and thermogenesis in mice.

This study identifies three IGHV3-23 antibodies targeting influenza HA stem, showing that non-neutralizing antibodies with enhanced Fc-mediated effector functions offer better in vivo protection than a potent neutralizer.

This paper develops a coarse-grained model for simulating nascent polypeptide dynamics in the ribosome, enabling efficient simulation of elongation and escape processes.

This study determines the crystal structures of bacterial hydrazine synthetases and elucidates their mechanism, enabling the expansion of hydrazine biosynthesis through novel enzyme discovery and chemoenzymatic synthesis.

This study identifies a monoclonal antibody that neutralizes HCoV-HKU1 by mimicking sialic acid binding to block receptor engagement.

This study investigates how the alarmones ppGpp and pppGpp differentially regulate the nucleosidase PpnN in E. coli, revealing its role in bacterial survival under antibiotic stress and uncovering a conserved catalytic mechanism shared with plant cytokinin signaling proteins.

An atom-level graph neural network that denoises corrupted structures generates small-molecule and protein-ligand conformational ensembles, and its active-site pre-organization metric enriched for more active designed retroaldolases.

The paper analyzes SARS-CoV-2 spike structures to propose a general RBD-rising pathway that describes crown-opening dynamics and antibody-binding effects.

This study compares intrinsic dynamics of PAS domains in bHLH-PAS transcription factor complexes using ENMs and MD simulations, revealing conserved self-coupled motions and context-specific directly coupled motions.

The paper uses molecular dynamics simulations to study how DNA sequence and superhelical density affect structural dynamics in minicircles, finding that undercoiling leads to stable denaturation bubbles.

The paper introduces a coarse-grained MD approach to simulate competitive ligand binding at the adenosine A2A receptor, revealing cooperative mechanisms in ligand competition.

This study identifies how ultrapotent antibodies neutralize SARS-CoV-2 by distributing binding energy across rigid interfaces, enabling tolerance to mutations and informing therapeutic design.

This paper uses neutron crystallography to determine the structure of β-glucosidase Td2F2 in different ligand states, revealing hydrogen bonding networks and structural changes in the catalytic center during covalent intermediate formation.

This study investigates the role of the ACT domain in prephenate dehydrogenase (PDH) allosteric regulation and its evolutionary significance in bacterial metabolic adaptation.

This study reveals an atypical activation mechanism of CXCR7, identifies its role as an opioid receptor, and highlights potential for novel pain therapeutics.

This study characterizes the conformational preferences of C-terminal tails in GroEL, mHsp60, and Cpn60 using spectroscopy, revealing they adopt polyproline II helices rather than being fully disordered.

This study determines the cryo-EM structure of the Drosophila Alka channel, revealing a lysine residue as a molecular switch for alkaline pH sensing and identifying hydroxide ions as a new class of ion channel ligands.

The paper identifies antiviral resistance mutations in chikungunya virus envelope proteins that reveal a transient functional interaction between distal domains during fusion.

This study reveals a three-step mechanism of co-transcriptional H3K36 methylation by SETD2 through cryo-EM structures and functional analysis.