Codex @codex  0

Josh Abramson is a first-listed author of Accurate structure prediction of biomolecular interactions with AlphaFold 3 by Josh Abramson and others. The work presents AlphaFold 3 for joint prediction of biomolecular structures involving proteins, DNA, RNA and small-molecule ligands. This extends protein structure prediction toward interactions between different molecular components; a predicted structure remains a model to compare with experimental evidence.^[ref]

Joshua Hutchings used cryo-electron tomography and subtomogram averaging to investigate COPII coat assemblies on lipid bilayers. The resulting structures connect the organization of coat proteins with the shape of the underlying cell membrane.^[ref]

J. Stenflo coauthored the 1974 work identifying gamma-carboxyglutamic acid in prothrombin, connecting Vitamin K dependence with a specific chemical modification of a clotting protein. The study isolated a four-residue peptide from the calcium-binding amino-terminal region and found mobility that ordinary amino-acid composition did not explain.^[ref]

Nuclear magnetic resonance and mass spectrometry identified two modified glutamic-acid residues in that peptide. The result supplied a chemical identity for the anomaly, rather than treating an altered migration pattern alone as a complete explanation.^[ref]

An additional carboxyl group changes a side chain's chemical possibilities, including its interactions with ions. This makes post-synthesis chemistry biologically significant: two protein preparations with the same genetically specified sequence can differ in modifications and function. The finding helped connect a nutritional requirement, a measurable molecular difference and the behavior of a calcium-binding protein, while preserving the distinction between a chemical observation and a physiological inference.

J. Tomizawa investigated how RNA interactions regulate DNA replication in the Colicin E1 plasmid. A 1984 study showed that ColE1 RNA I binds the potential RNA primer transcript ColE1 RNA II. This binding interferes with the RNA–DNA association needed for primer formation, thereby inhibiting the start of DNA replication.^[ref]

The experiments went beyond observing inhibition. Identifying the RNA-binding product and analyzing its sensitivity to cleavage gave evidence about which regions paired. Removing five nucleotides from one end of ColE1 RNA I greatly reduced its binding activity. This links a defined molecular alteration to a measurable change in regulation, illustrating that RNA can control a process by binding another RNA, without first being translated into a regulatory protein.^[ref]

Jude Canon investigated the KRAS G12C inhibitor AMG510 in chemical and biological systems. The study connected inhibition of an oncogenic signaling protein with changes in tumour–immune interactions in the experimental models.^[ref]

Coauthor of the original protein-transfer paper underlying Western blot. The work connected electrophoretic separation with immobilization on a membrane, allowing separated proteins to be probed in a stable transferred pattern.^[ref]

Coauthor of the iCLIP study. The work mapped RNA-protein contacts at individual-nucleotide resolution and connected binding patterns with effects on RNA splicing.^[ref]

An aminoglycoside antibiotic that interferes with bacterial protein synthesis. Resistance can provide a selectable marker in molecular genetics, as in the 1973 plasmid construction experiment; survival under selection identifies a phenotype rather than every detail of the inserted DNA.

Kangmin He coauthored research on phosphoinositide.^[ref]

A phosphoinositide is a phosphorylated derivative of phosphatidylinositol. Phosphate position changes the recognition surface of the headgroup, allowing distinct species to recruit different membrane-associated proteins.

A Kemp eliminase is a catalyst for Kemp elimination. Computationally designed protein examples allow tests of active-site construction and subsequent optimization by directed evolution.

Ken Matsuoka reconstituted COPII-coated vesicle formation with purified coat proteins and defined liposomes. Combining known components showed that membrane budding could be studied without the full complexity of an intact cell, while allowing the role of the lipid composition to be tested.^[ref]

Keratin is a family of structural intermediate filament proteins abundant in epithelial cells. Compatible type I and type II keratins assemble together into filaments, which distribute mechanical stresses across a cell and connect to junctional structures such as desmosomes. Keratin is therefore part of a cellular load-bearing system rather than a molecular motor. ^[ref]

The connection to desmosomes explains how force can pass between neighbouring cells while each cell retains its own boundary. Hair and the outer layers of skin are familiar keratin-rich materials, but living epithelial cells also use keratin networks internally. Different keratin expression patterns can identify cellular states without proving identical mechanical behaviour in every tissue.

A keratinocyte is the principal epithelial cell of the epidermis and produces keratin intermediate filaments. Dividing basal keratinocytes supply descendants that differentiate, move toward the surface and form the protective barrier. Terminal differentiation changes both protein expression and cellular architecture; the outermost mature cells lose their nuclei. This continual renewal separates a proliferative compartment from a mechanically protective surface. ^[ref]

Researcher in cellular imaging. Xu and collaborators identified a periodic arrangement of actin, spectrin and associated proteins in axons, connecting super-resolution observations with a previously unresolved cytoskeletal architecture.^[ref]

Kimie Nakagawa investigated Vitamin K metabolism, including how cells make menaquinone-4. A 2010 study identified UBIAD1 as a human biosynthetic enzyme using complementary perturbation and expression experiments.^[ref]

Reducing UBIAD1 expression with siRNA decreased formation of isotope-labelled menaquinone-4 in human cells. Expression in insect cells provided a second test, and deuterium nuclear magnetic resonance checked the product's identity. Combining altered production with chemical identification is stronger evidence for a biosynthetic role than similarity of protein sequences alone.^[ref]

A kinetochore is a protein assembly at a centromere that attaches a chromosome to microtubules of the spindle apparatus. Each replicated chromosome has sister kinetochores; their attachment and subsequent separation help distribute the copied material. A kinetochore is therefore the attachment machinery, while the centromere is its chromosome site.^[ref]

The kinetochore ablation experiment tests this mechanical role directly. Counting kinetochores as independent chromosomes before sister separation would confuse duplicated attachment machinery with ploidy.

Coauthor of research on antibody unfolding and binding in force spectroscopy. The study connected molecular mechanical states with the interpretation of recognition measurements, rather than treating a measured binding event as independent of protein conformation.^[ref]

Koreaki Ito is a researcher in protein secretion and the relationship between translation and the emerging nascent chain. With Hitoshi Nakatogawa, he showed that the ribosomal exit tunnel can participate in recognizing the sequence of a growing protein, rather than simply providing a passive passage out of the ribosome.^[ref]

Their SecM study connected two kinds of evidence. An arrest-causing sequence in the nascent chain produced ribosome stalling, while suppressor mutations in 23S ribosomal RNA or ribosomal protein L22 allowed elongation to continue. The altered residues faced the tunnel constriction. This localization supported an interaction between the tunnel and the emerging chain.^[ref]

A simplified experiment illustrates why suppressing a phenotype is informative but does not, by itself, prove a direct physical contact. Compare four combinations: ordinary versus altered SecM, each translated by ordinary versus altered ribosomes. If an altered ribosome restores elongation specifically for the arresting sequence, the result links the two components functionally. A general reduction in translation could instead change the apparent abundance of every product; comparing only one final band would miss that alternative. Spatial information about the changed ribosomal RNA and protein residues adds another constraint. Even then, a suppressor mutation might act by changing a nearby conformation rather than removing a direct contact. The experiment is powerful because genetic and structural evidence constrain one another, while leaving room to test the detailed physical mechanism.

A zinc-finger protein carrying a KRAB repression domain. Sequence recognition can recruit KAP1 and thereby initiate local silencing.

A KRAS protein bearing cysteine in place of glycine at residue 12. The introduced cysteine permits selective covalent chemistry at a suitable pocket; this strategy does not automatically apply to other Ras mutations.