Proceedings of the National Academy of Sciences
Articles in this Issue
Predicting gene sequences with AI to study codon usage patterns
Selective pressure acts on the codon use, optimizing multiple, overlapping signals that are only partially understood. We trained AI models to predict codons given their amino acid sequence in the euk...
Topological confinement by a membrane anchor suppresses phase separation into protein aggregates: Implications for prion diseases
Protein misfolding and aggregation are a hallmark of various neurodegenerative disorders. However, the underlying mechanisms driving protein misfolding in the cellular context are incompletely underst...
Quantifying the genetic origins of body plan scaling
The origin of color categories
To what extent does concept formation require language? Here, we exploit color to address this question and ask whether macaque monkeys have color concepts evident as categories. Macaques have similar...
Pseudogap in electron-doped cuprates: Strong correlation leading to band splitting
The pseudogap phenomena have been a long-standing mystery of the cuprate high-temperature superconductors. The pseudogap in the electron-doped cuprates has been attributed to band folding due to antif...
Protein dynamics underlies strong temperature dependence of heat receptors
Ion channels are generally allosteric proteins, involving specialized stimulus sensor domains conformationally linked to the gate to drive channel opening. Temperature receptors are a group of ion cha...
Tungsten is utilized for lactate consumption and SCFA production by a dominant human gut microbe <i>Eubacterium limosum</i>
Eubacterium limosum is a dominant member of the human gut microbiome and produces short-chain fatty acids (SCFAs). These promote immune system function and inhibit inflammation, ma...
Integrating climate and physical constraints into assessments of net capture from direct air capture facilities
Limiting climate change to targets enshrined in the Paris Agreement will require both deep decarbonization of the energy system and the deployment of carbon dioxide removal at potentially large scale...
Genesis and regulation of C-terminal cyclic imides from protein damage
C-Terminal cyclic imides are posttranslational modifications that can arise from spontaneous intramolecular cleavage of asparagine or glutamine residues resulting in a form of irreversible protein dam...
Mechanism-guided engineering of a minimal biological particle for genome editing
The widespread application of genome editing to treat and cure disease requires the delivery of genome editors into the nucleus of target cells. Enveloped delivery vehicles (EDVs) are engineered viral...
Structural insight into sodium ion pathway in the bacterial flagellar stator from marine <i>Vibrio</i>
Many bacteria swim in liquid or swarm on surface using the flagellum rotated by a motor driven by specific ion flow. The motor consists of the rotor and stator, and the stator converts the energy of i...
Palmitoylation-dependent association with Annexin II directs hepatitis E virus ORF3 sorting into vesicles and quasi-enveloped virions
Historically considered to be nonenveloped, hepatitis E virus (HEV), an important zoonotic pathogen, has recently been discovered to egress from infected cells as quasi-enveloped virions. These quasi-...
Profile of Stefan W. Hell
Modular DNA origami–based electrochemical detection of DNA and proteins
The diversity and heterogeneity of biomarkers has made the development of general methods for single-step quantification of analytes difficult. For individual biomarkers, electrochemical methods that...
Geometrically modulated contact forces enable hula hoop levitation
Mechanical systems with moving points of contact—including rolling, sliding, and impacts—are common in engineering applications and everyday experiences. The challenges in analyzing such systems are c...
Across the firewall: Foreign media’s role in shaping Chinese social media narratives on the Russo-Ukrainian War
There is a widespread perception that China’s digital censorship distances its people from the global internet, and the Chinese Communist Party, through state-controlled media, is the main gatekeeper...
Oppositional and competitive instigation of hippocampal synaptic plasticity by the VTA and locus coeruleus
The novelty, saliency, and valency of ongoing experiences potently influence the firing rate of the ventral tegmental area (VTA) and the locus coeruleus (LC). Associative experience, in turn, is recor...
Electron transfer in polysaccharide monooxygenase catalysis
Polysaccharide monooxygenase (PMO) catalysis involves the chemically difficult hydroxylation of unactivated C–H bonds in carbohydrates. The reaction requires reducing equivalents and will utilize eith...
Unlocking the catalytic precision of ligand-controlled enzymatic halogenation
A single-component flavin-dependent halogenase, AetF, has emerged as an attractive biocatalyst for catalyzing halogenation. However, its flavin chemistry remains unexplored and cannot be predicted due...
Income inequality and the erosion of democracy in the twenty-first century
Among the most pressing problems societies face today are economic inequality and the erosion of democratic norms and institutions. In fact the two problems—inequality and democratic erosion—are linke...
A hybrid meta on-top functional for multiconfiguration pair-density functional theory
Multiconfiguration pair-density functional theory (MC-PDFT) was proposed a decade ago, but it is still in the early stage of density functional development. MC-PDFT uses functionals that are called on...
Synapse-specific catecholaminergic modulation of neuronal glutamate release
Norepinephrine in vertebrates and its invertebrate analog, octopamine, regulate the activity of neural circuits. We find that, when hungry, Drosophila larvae sw...
Tetrameric PilZ protein stabilizes stator ring in complex flagellar motor and is required for motility in <i>Campylobacter jejuni</i>
Rotation of the bacterial flagellum, the first identified biological rotary machine, is driven by its stator units. Knowledge gained about the function of stator units has increasingly led to studies...
Deep conservation complemented by novelty and innovation in the insect eye ground plan
A spectacular diversity of forms and features allow species to thrive in different environments, yet some structures remain relatively unchanged. Insect compound eyes are easily recognizable despite d...
Learning the language of antibody hypervariability
Protein language models (PLMs) have demonstrated impressive success in modeling proteins. However, general-purpose “foundational” PLMs have limited performance in modeling antibodies due to the latter...