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A phycobilin is a light-absorbing linear tetrapyrrole chromophore associated with particular photosynthetic antenna proteins. Its extended conjugated framework absorbs visible light.

Different phycobilin-containing complexes absorb different spectral regions, including wavelengths used less effectively by chlorophyll a. The chromophore's chemical structure and its protein environment jointly shape the observed spectrum.

A family of light-sensing proteins with interconvertible red-absorbing and far-red-absorbing forms. Phytochrome links light perception to plant development, including the lettuce red and far-red germination experiment.^[ref]

A maternally supplied protein segregating to germline blastomeres in Caenorhabditis elegans, where it suppresses inappropriate somatic transcription.

Pilong Li investigated phase separation produced by interactions among multivalent signaling proteins. The study connected the onset of droplet formation with a transition from small complexes to large assemblies, and related the threshold to the number of interaction sites.^[ref]

A guide RNA associated with Piwi-family proteins. Most characterized animal piRNA pathways use Dicer-independent processing of single-stranded precursors; the approximately 21-nucleotide C. elegans 21U RNAs are distinct from the longer typical fly and mammalian piRNAs.^[ref]

Coauthor of experiments linking GTP-binding proteins with activation of a potassium current by cardiac muscarinic receptors. The study connected receptor stimulation with an intervening signaling mechanism rather than direct receptor–channel identity.^[ref]

A plasma protein is a protein present in blood plasma. Transport, immune functions, coagulation and osmotic effects are among their different roles. Total protein concentration does not specify the amount or activity of any one component.

Plasmin is a protease that cuts fibrin into soluble products, helping dismantle a blood clot. It is produced by proteolytic activation of plasminogen, an inactive precursor. Activation of an existing precursor can switch on an enzymatic process without waiting for new protein synthesis.^[ref]

This supplies a useful contrast within clot biology. Thrombin helps form the fibrin network; plasmin helps remove it. In a simplified experiment, a fibrin gel can therefore be formed first and its subsequent breakdown measured after adding active plasmin. The observable loss of the network is a consequence of peptide bond cleavage, linking a molecular reaction to a macroscopic change in material structure.

The protein plasminogen is the inactive precursor of plasmin, a protease that helps break down fibrin in a blood clot. Activation requires cleavage of a particular peptide bond, converting an abundant circulating precursor into an active enzyme. Production of the precursor and activation of that precursor are therefore separate control points. ^[ref]

A useful measurement distinction follows: a sample can contain substantial plasminogen yet have little ongoing proteolysis. An assay that supplies an activator tests potential activity under those assay conditions; it does not directly report the original rate of clot breakdown. Local activation and inhibition help confine protease action to appropriate sites.

A plasmodesma, plural plasmodesmata, is a membrane-lined connection crossing a plant cell wall between neighboring cells. It provides a route for intercellular exchange, including movement of some signaling molecules and macromolecules. A plasmodesma contains a tubular strand of endoplasmic reticulum within its enclosing cell membrane; it is an organized cellular interface, rather than simply a hole in the wall.^[ref]

Transport changes during development. A cotton fibre study followed a fluorescent tracer from the seed coat into elongating fibres with confocal microscopy. Access through plasmodesmata was observed early, blocked around day 10 and observed again around day 16. Reverse tracer movement supplied a complementary test, distinguishing transport connectivity from the mere presence of a channel in a section.^[ref]

The apparent width in an image is not the whole explanation of permeability. A 2017 electron tomography study found newly formed plasmodesmata with no visible open cytoplasmic sleeve, yet observed macromolecular diffusion. Architecture and transport must therefore be measured together.^[ref]

An original comparison would score channel number, three-dimensional structure and transfer of a defined tracer separately. Equal channel counts do not guarantee equal exchange, and passage of one tracer does not establish unrestricted passage of every protein.

PDGF means platelet-derived growth factor, a family of signaling protein ligands for PDGFR. Members form protein dimers, including the classical AA, AB and BB combinations.^[ref] Ligand binding can bring two receptors together and activate their receptor tyrosine kinase activity.^[ref]

Release from platelets links PDGF to local tissue responses after injury. Nearby connective-tissue cells can respond by entering cell proliferation.^[ref]

Pmel17 is a pigment-cell glycoprotein that helps build the internal scaffold of developing melanosomes, the organelles in which melanin is produced and stored. It is synthesized as a membrane protein, but processing produces a large lumen-facing component associated with the characteristic internal striations of immature melanosomes. The scaffold and the pigment deposited on it are different materials.

Joanne F. Berson and colleagues expressed Pmel17 in nonpigmented cells. Electron microscopy revealed striation-like structures inside multivesicular bodies, compartments that normally lack the specialized pigment-cell architecture. Together with localization and processing experiments in pigmented cells, this supported a direct role for Pmel17 in constructing the melanosome interior. It demonstrates how adding a particular protein can reshape a general intracellular compartment into a specialized organelle.^[ref]

Podocalyxin is a heavily glycosylated cell-surface protein involved in apical organization and cell-surface properties. It is prominent in kidney podocytes and is also used to follow apical membrane formation in epithelial models. Its charged extracellular region and intracellular connections contribute different properties. Localization can reveal polarity, but demonstrating that podocalyxin causes a polarity change requires a perturbation and functional readout. ^[ref]

A podocyte foot process is a fine extension of a podocyte that lies against the glomerular basement membrane. Neighboring podocyte foot process structures interdigitate, leaving narrow filtration slits crossed by a slit diaphragm. The podocyte is one whole epithelial cell; its many processes collectively shape part of the glomerular filtration barrier.

An electron microscope section makes the distinction concrete: identify the basement membrane, then the small profiles resting on its outer side, then the gaps between those profiles. A profile is not necessarily a separate cell; multiple profiles can belong to branches of one podocyte. Conversely, the gap between two profiles is not itself a podocyte foot process.

In a 1999 study, immunogold labeling placed nephrin at the slits between these processes. Figure3 includes sections across the slit and a tangential view with a row of gold particles. Combining the label with the local geometry helped locate a protein at a junction rather than merely somewhere in the glomerulus.^[ref]

A protein that binds a poly(A) tail and can influence messenger RNA stability and biological translation.

A stretch of adenosine-containing residues at an RNA end. Tail length and associated proteins can influence messenger RNA stability and biological translation.

Transcriptional repression mediated by Polycomb-group proteins and associated chromatin states. Developmental regulators can be kept inactive until appropriate activation.

A polypeptide is a chain of amino acid residues linked by peptide bonds. The term describes chain chemistry; calling a chain a polypeptide alone does not establish that it is folded or functional. The gene expression example N–methionine–alanine–C contains two amino acid residues and one peptide bond; the twelve-residue example under protein contains eleven peptide bonds. See IUPAC-IUB: amino-acid symbols and representation of residues in chains.

Polyproline is a chain or sequence region enriched in repeated proline residues. Proline constrains backbone geometry, and some proline-rich regions adopt an extended polyproline-II conformation. Such regions can serve as recognition elements for interaction domains in signalling proteins. Sequence enrichment, conformation and binding function should be distinguished: a proline-rich segment does not automatically establish one fixed structure or partner. ^[ref]

A polyprotein is a polypeptide chain that supplies several protein products through proteolysis. One translation product can therefore contain the sequences of multiple eventual products. This differs from a protein complex assembled by association of independently made chains.

The relationship can be tested by mapping product sequences back onto a precursor. In 1981, investigators determined the poliovirus RNA sequence and identified a long open reading frame. Amino acid sequence analysis mapped twelve viral polypeptides to cleavage products of the encoded polyprotein. Agreement between the sequence and the isolated products supported a common precursor, rather than merely grouping similar-sized bands together.^[ref]

For an original accounting example, suppose a hypothetical precursor consists of consecutive regions of 200, 150 and 250 amino acid residues. Two cuts at the boundaries can yield three chains containing 600 residues altogether. Cleavage increases the number of molecules without synthesizing additional amino acid residues. Partial processing would also produce intermediates containing more than one of the regions.

The precursor and the final products need not have identical functions or lifetimes. An assay recognizing a sequence retained in several intermediates can detect more than one molecular species. Identifying a polyprotein thus requires following both its protein primary structure and its processing state.