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A switch-complex protein involved in reception of phosphorylated CheY and control of rotational bias.

Binding of phosphorylated CheY changes the switch’s rotational bias. A change in bias alters the balance of swimming behaviours without requiring the motor to sense external attractant directly. ^[ref]

Florian C. Oberstrass investigated the structure of the polypyrimidine tract-binding protein bound to RNA. The work connected sequence recognition with the arrangement of RNA-binding domains and the regulation of RNA splicing.^[ref]

Flowering is the transition to producing flowers, the reproductive structures of angiosperms. A meristem that previously produced vegetative organs begins a developmental program forming flowers. This transition can precede the visible opening of a flower, called anthesis, by a substantial interval.

Photoperiodism links flowering to seasonal day length. In Arabidopsis thaliana, the timing of CONSTANS gene expression and the stabilization of its protein by evening light allow long days to promote flowering. Experiments measuring CONSTANS abundance showed that a daily rhythm in messenger RNA alone did not explain the response: light-dependent protein degradation supplied another regulatory step.^[ref] Different plants integrate different combinations of day length, temperature and developmental state; flowering is not triggered by one universal environmental threshold.

The fluid mosaic model describes a cell membrane as a fluid lipid bilayer with embedded membrane proteins. It connects a continuous barrier to a mosaic of functional components: diffusion within the membrane can coexist with selective passage across it. S. J. Singer and G. L. Nicolson presented the fluid mosaic model in Science in 1972; see Singer and Nicolson, The fluid mosaic model of the structure of cell membranes. The useful picture does not require every protein to move freely: attachments and interactions can restrict movement, as discussed in Cooper, The Cell: structure of the plasma membrane.

A bacterial DNA-recognition pair marks an integrated operator array with a fluorescent repressor. It enables live tracking of a chosen genetic locus, while the array and bound protein can perturb that locus.

A genetically encodable protein that emits fluorescence after appropriate excitation. Fusion constructs can label cellular structures, but expression and illumination must be controlled for effects on the process being observed.

A folding funnel is a schematic energy landscape in which increasingly native-like protein conformations tend to have lower free energy, while the many unfolded conformations occupy a broad region. Roughness represents barriers and possible kinetic traps. The funnel is an organizing description, not a claim that every protein follows one unique geometrical trajectory or possesses a rigid isolated native state.

Förster resonance energy transfer is a nonradiative transfer of energy from an excited state of a FRET donor to a nearby FRET acceptor, through coupling of their electric dipoles. The transfer step does not emit a photon that the FRET acceptor subsequently absorbs. It competes with the FRET donor's own fluorescence and other routes out of its excited state. A fluorescent FRET acceptor can then emit fluorescence; an absorbing but nonfluorescent FRET acceptor can still receive the transferred energy.^[ref]

The striking use of FRET is to turn a change in molecular proximity into an optical readout. Proteins carrying a FRET donor and a FRET acceptor may change the readout when they associate, as in the chemotaxis FRET assay; two labels on one protein may report a change in its shape. Interpretation depends on the FRET spectral overlap, FRET dipole orientation factor and labeling geometry, as well as separation. A change in FRET is therefore evidence about proximity under specified conditions, rather than a direct measurement of an arbitrary distance.^[ref]

For a single pair with fixed Förster distance $R_0$ and label separation $r$, the FRET efficiency isAt $r=R_0$, half the FRET donor excitations transfer energy. At $r=R_0/2$, the model gives $E=64/65\approx 98.46\%$; at $r=2R_0$, it gives $E=1/65\approx 1.54\%$. The sixth power makes FRET especially useful near the Förster distance, with little sensitivity to further separation once transfer is already negligible. These are model calculations, not measurements of a particular pair.

The Fc fragment comprises paired immunoglobulin heavy chain $C_{H2},C_{H3}$ portions, interacts with immune partners and lacks paratopes. Its name records historical crystallization.^[ref]

For example, Fc fragments can bind components of the complement system, illustrating a function distinct from epitope recognition.^[ref]

An isolated Fc fragment therefore separates one set of protein interactions from target recognition. In the connectivity example under Papain digestion of IgG, the Fc fragment contributes one connected product but zero antibody binding sites. Retaining it preserves different interaction surfaces; it does not restore either severed arm. Conversely, the two Fab fragments preserve the stipulated epitope-recognition sites while losing their connection to this common stem.

Franz Hagn coauthored research on membrane protein.^[ref]

A membrane protein is a protein associated with a biological membrane. Its association, orientation and mobility are separate properties: being embedded does not imply spanning, and spanning does not imply moving freely. Membrane proteins supply routes for membrane transport and recognition for signal transduction.

Frederick Sanger coauthored DNA sequencing by chain termination. Incorporation of a chain-terminating nucleotide creates fragments whose lengths report the positions of a particular base.

Resolving fragments by length converts a biochemical copying reaction into sequence information. The key chemical distinction is that a terminating nucleotide lacks the group required for continued chain extension.^[ref]

A biochemist known for protein and DNA sequencing, including Sanger sequencing.

Nobel Prize record: www.nobelprize.org/nomination/archive/show_people.php?id=8092

The FRET dipole orientation factor describes the geometry of the two transition electric dipoles relative to their separation. Let ${\hat{\mathbf{\mu }}}_D$, ${\hat{\mathbf{\mu }}}_A$ and $\hat{\mathbf{r}}$ be their unit vectors. ThenFor a separation along $z$, parallel electric dipoles along $z$ give ${\kappa }^2=4$, parallel ones along $x$ give $1$, and one along $x$ with the other along $y$ gives $0$. Thus rotating a pair can change FRET efficiency without changing its separation.

The familiar value ${\kappa }^2=2/3$ requires suitable rapid, independent orientation averaging during the FRET donor lifetime. Random orientations across a population of slowly rotating fluorescent proteins do not establish that dynamic condition. ^[ref]

FRET optical crosstalk includes FRET donor emission leaking into the FRET acceptor detection band and direct excitation of the FRET acceptor by the nominal FRET donor excitation light. Measure donor-only, acceptor-only and unlabeled preparations with the same fluorescence microscope settings to separate these contributions and background.^[ref]

An explicit linear measurement model makes the controls' purpose clear. Let $D$ be background-subtracted donor-band counts under donor excitation, $A$ acceptor-band counts under acceptor excitation, and $F$ acceptor-band counts under donor excitation. Donor-only and acceptor-only preparations determine leakage coefficients $a$ and $b$. Thenis a corrected FRET sensitized emission signal under the assumed linear, fixed optical response. In a synthetic example $D=100$, $A=80$, $a=0.10$, $b=0.05$ and $F=34$ give $S=20$. Even a nontransferring sample would give $F=14$ from these two contaminants. Correcting that signal still does not convert $S$ into FRET efficiency without a calibration of excitation, yields and detection.

A biological comparison also needs a pairing-negative preparation and a known transferring positive preparation. Match label abundance and localization where possible; changing concentration can change encounter frequency as well as brightness. Check that attaching the labels preserves the protein function being investigated. Otherwise the measurement can faithfully report a perturbation introduced by the labels themselves.

A paleontologist who used ancient protein sequences to test evolution relationships of extinct South American ungulates, illustrating palaeoproteomics when recoverable DNA is unavailable.^[ref]

Experimental Reconstruction of Functional Gene Transfer from the Tobacco Plastid Genome to the Nucleus by Sandra Stegemann and Ralph Bock (2006, Results, pp. 2870–2874) separated relocation of DNA from activation of a relocated gene. Engineered tobacco chloroplasts carried an nptII gene with nuclear expression signals beside an aadA gene with plastid expression signals. Selection on kanamycin recovered plants with the segment in the nuclear genome. Crosses then replaced the engineered chloroplasts with ordinary chloroplasts: the nuclear segment remained, but the plants were initially sensitive to spectinomycin and streptomycin. The transferred aadA gene was not yet functional in its new setting.

Leaf pieces were cultured on regeneration medium containing both drugs. Resistant regenerated plants supplied the functional readout. Using both drugs reduced selection of spontaneous plastid mutations conferring resistance mainly to one drug. Reciprocal crosses and selfing distinguished maternal plastid inheritance from nuclear Mendelian segregation; eight of sixteen initial candidates had the latter pattern. ^[ref]

The molecular readout came from RNA hybridization and DNA sequencing. A Northern blot detected aadA messenger RNA in activated lines, with different transcript sizes. Thermal asymmetric interlaced polymerase chain reaction recovered upstream DNA; products present in activated lines but absent in original-line and ordinary-plant controls were sequenced. The mapped rearrangements connected aadA to the upstream nuclear gene promoter. Thus resistance, inheritance, RNA detection and changed nucleotide sequences supported activation of the transferred nuclear gene, rather than resistance alone. ^[ref]

This engineered test demonstrates one route to functional nuclear gene expression after plastid DNA transfer. It does not establish a natural transfer rate, replay ancient endosymbiosis or demonstrate that the resulting protein is imported into a chloroplast. The authors explicitly identify acquisition of targeting information as an additional step not reproduced by this experiment. ^[ref]

Researcher in molecular biology. Studier and collaborators used bacteriophage T7 RNA polymerase to direct high expression of cloned genes, exploiting selective promoter recognition to control recombinant protein production.^[ref]

An RNA-associated regulator of stress-granule assembly. Requirements for assembly depend on stress and partner context.

Like G3BP2, it can organize interactions among RNA and proteins during stress-granule formation. Perturbing those interactions distinguishes a direct assembly requirement from mere co-localization in an already formed granule. ^[ref]

A gamma-carboxyglutamate residue, or Gla residue, is a glutamate residue within a protein whose side chain carries an additional carboxyl group at its gamma carbon. It is the protein-bound form associated with gamma-carboxyglutamic acid. The amino acid residue remains part of the polypeptide backbone; the modification changes its side chain.

The distinction from the free amino acid matters experimentally. Identifying gamma-carboxyglutamic acid after breaking a protein into smaller components reveals chemical composition, while determining which residues are modified and how they are arranged requires structural or sequence evidence.^[ref]

In a Gla domain, multiple Gla residues help coordinate calcium ions. A 1992 X-ray crystallography study of a prothrombin fragment resolved seven bound calcium ions in its calcium-bound structure and found substantial disorder in the corresponding calcium-free region. This illustrates how a local chemical modification can contribute to an ion-dependent folded arrangement.^[ref]

Gamma-carboxyglutamic acid is a derivative of glutamic acid with an additional carboxyl group attached at the gamma carbon of the side chain. Its side chain can be written $-\mathrm{C}{\mathrm{H}}_2-\mathrm{CH}(\mathrm{COOH}{)}_2$ in the fully protonated representation. The extra carboxyl group changes the ion-binding properties of the corresponding gamma-carboxyglutamate residue within a protein.

In 1974, J. Stenflo and colleagues identified this unusual amino acid in prothrombin. Anomalous electrophoresis behaviour led to analysis by nuclear magnetic resonance and mass spectrometry, connecting a chemical modification with the special properties of this clotting protein.^[ref]

An illuminating comparison is to count the side-chain acid groups: glutamic acid has one, while gamma-carboxyglutamic acid has two. Their ionized forms provide additional negatively charged oxygen donors for calcium ions. The arrangement of several modified residues in a folded Gla domain gives the protein its calcium-binding architecture; an isolated modified amino acid is only one component of that structure.^[ref]

A ribosome-associated regulator supporting activation of GCN2 during nutrient stress.

Association with translating ribosomes links the signalling machinery to the state of protein synthesis. The response can reduce general initiation while favouring specific stress-regulated outputs, coupling nutrient availability to translational control. ^[ref]