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A protein phosphatase is an enzyme that removes a phosphate group from a modified protein through hydrolysis. This restores a modifiable site rather than regenerating ATP by simply running protein kinase chemistry backward.

Protein phosphatase 1 catalyses protein dephosphorylation in regulated complexes. Association with targeting partners matters: effects on one substrate do not imply indiscriminate dephosphorylation of all cellular proteins.

The protein primary structure specifies the ordered amino acid residues of each polypeptide chain, joined through peptide bonds. A chain is conventionally written from its N-terminus to its C-terminus. In the broader chemical sense, a complete protein primary structure also specifies covalent bond crosslinks between chain positions, including protein disulfide bonds; a bare sequence string leaves that information unstated. This describes chemical connectivity rather than the spatial arrangement of protein tertiary structure or protein quaternary structure. See IUPAC Gold Book: primary structure, sequence and chain crosslinking and IUPAC-IUB, 3AA-16: writing residue sequences from the amino end. Some conventions reserve protein primary structure for sequence alone and call the complete chemical connectivity the covalent structure; the distinction should be stated when comparing descriptions. See IUPAC-IUB polypeptide-conformation recommendations, section 6.1: the narrower sequence-only convention.

In this toy example M denotes methionine, A alanine and G glycine. Both polypeptide chains have six amino acid residues, five peptide bonds, an M at the N-terminus and a G at the C-terminus. Their amino acid composition is identical, yet position 2 is A in MAGAMG and M in MMAAGG. There are $6!/(2!2!2!)=90$ distinct orders with these counts, a multinomial coefficient. Even fixing those two end residues leaves $4!/(1!2!1!)=12$ orders. The counts constrain the answer without determining it.

For multiple polypeptide chains, record each sequence separately and specify any protein disulfide bonds between cysteine positions. Mature insulin, for example, has an A chain of 21 amino acid residues and a B chain of 30 amino acid residues. Their combined 51 residues give $(21-1)+(30-1)=49$ peptide bonds, rather than the 50 of one unbroken 51-residue chain. See Cooper, The Cell: insulin's two chains and cysteine crosslinks, figure 2.16. A protein disulfide bond joins side groups; it does not concatenate the C-terminus of one chain with the N-terminus of another. The three insulin protein disulfide bonds connect A6 to A11 within the A chain, and A7 to B7 and A20 to B19 between chains. Positions are numbered from each chain's N-terminus. See Replacement of the interchain disulfide bridge-forming amino acids A7 and B7 by glutamate impairs the structure and activity of insulin: native disulfide positions.

Why keep this information? Protein primary structure lets us distinguish changes of chemical identity from changes of shape, and compare corresponding positions between proteins. Protein folding can bring distant amino acid residues together at a protein binding site while preserving their sequence. The attractive idea is that a readable linear record can constrain a complicated three-dimensional object; it is not, by itself, a guarantee of a unique fold in every environment. See protein folding and the ribonuclease A refolding experiment. Merely bending an intact chain preserves its protein primary structure; hydrolysis of a peptide bond, or changing which positions a protein disulfide bond connects, changes its chemical connectivity.

A protein-protein interaction is an association between proteins through physical contact. Copurification or proximity labeling can suggest an association without establishing that the measured pair contacts directly.

A protein-protein interaction network represents proteins as nodes and recorded interactions as edges. Direct physical binding, membership of a larger complex and functional association are different edge meanings and should be distinguished. A highly connected node can reflect biology, experimental sampling or both. The network is useful for proposing coordinated functions, but an edge alone does not identify binding affinity, direction of signalling or simultaneous occupancy. ^[ref]

Protein purification separates a selected protein from other components of a sample while recovering material useful for a subsequent measurement or application. Different procedures exploit different properties. In affinity chromatography, a matrix-bound ligand selectively retains the target through a reversible interaction.^[ref]

An enzyme example separates recovery from enrichment. Suppose a starting fraction contains $10\mathrm{mg}$ total protein and $200$ measured activity units, while a collected fraction contains $2\mathrm{mg}$ and $120$ units. The specific activity rises from $200/10=20$ to $120/2=60$ units per milligram: a threefold increase. Recovery of activity is $120/200=0.60$, or $60\%$. These are constructed assay values, not reported experimental data.

The preparation can therefore be enriched even while some target activity is lost. That inference assumes the assay reports the same catalytic property under comparable conditions; activation or inhibition can change activity without an equivalent change in protein amount. Protein purification consequently needs a stated target, an identity or activity measurement, and a recovery criterion. A visually clean fraction alone does not establish that its protein remains functional.

The protein quaternary structure is the arrangement of multiple polypeptide chains in a functional assembly. A single-chain protein has protein tertiary structure without requiring protein quaternary structure. For an exact bookkeeping example, two intact model chains of twelve amino acid residues each contain $2\times 12=24$ residues and $2\times 11=22$ peptide bonds. Assembly alone adds no peptide bond joining their ends. Stable functional assembly should also be distinguished from protein aggregation. See Alberts et al.: proteins as assemblies of polypeptide subunits.

Delivery of a protein from its producing cell to the extracellular environment, enabling communication and extracellular functions.

For fixed length $n$ and the standard twenty-amino-acid alphabet, there are $20^n$ sequences: each position has twenty choices. This counts possible sequences, not stable protein folds; the sequence-to-structure relationship is many-to-one and some sequences do not form a stable folded protein.

Visualization of proteins through binding of a dye or another detectable label. Signal depends on the staining chemistry and response range, so equal visual darkness need not establish equal molar amounts of different proteins.

Protein structure describes both the chain's chemical organization and its spatial arrangement. Four levels answer different questions: protein primary structure gives the order; protein secondary structure gives recurring local patterns; protein tertiary structure gives one chain's overall arrangement; protein quaternary structure gives the assembly of multiple chains. These are levels of description, not four mandatory stages that every protein must pass through. See Clark, Douglas and Choi: four levels of protein structure.

Inference of a protein’s three-dimensional structure from information such as sequence, related sequences and known structures. A useful prediction includes an assessment of uncertainty; a confident local fold does not automatically establish a molecular interaction or biological function.

A protein subunit is an individual polypeptide component of a protein complex. The number of protein subunits counts chain copies, whereas the number of subunit types counts distinct kinds of chain. An assembly $A_2{B}_2$ has four protein subunits of two types. A protein domain is a region within a chain and need not be a separate protein subunit; the arrangement of several chains belongs to protein quaternary structure.

The alpha/beta tubulin heterodimer illustrates the distinction: it contains two related but different polypeptides, not two domains cut out of one chain. The 1998 electron-crystallographic model resolved the alpha/beta architecture at $3.7$ angstrom resolution, using zinc-induced tubulin sheets.^[ref]

Subunit counting can also become an optical experiment. In total internal reflection fluorescence microscopy, tagged membrane proteins can be observed as isolated fluorescent spots; successive photobleaching steps reveal individual fluorescent tags disappearing. Subunit counting in membrane-bound proteins by Maximilian H. Ulbrich and Ehud Y. Isacoff used this approach on membrane proteins expressed in frog oocytes. For NR1/NR3B receptor assemblies, tagging one component type mainly gave two steps, while tagging both gave four, supporting a two-plus-two arrangement.^[ref]

A count of visible steps need not equal the true number of protein subunits: some tags fail to fluoresce, and two tags may bleach too close together to resolve. The experiment therefore combines step counts with a model of labeling and detection, rather than interpreting every two-step trace as proof of a two-chain protein complex.^[ref]

Protein targeting directs a protein to its cellular destination. Synthesis in the cytosol does not imply that the protein works there.

For entry into the endoplasmic reticulum, distinguish three questions: does the nascent chain reach the membrane, does part of it cross into the ER lumen, and does a segment remain embedded as a transmembrane protein? Cotranslational protein translocation couples these events to biological translation. A signal peptide can initiate delivery without specifying the eventual destination of the mature protein.

This distinction matters experimentally. Finding a protein in a membrane-containing centrifugation pellet could reflect surface binding or protein aggregation. The microsomal protein import experiment instead asks whether an intact membrane prevents an external protease from reaching the product. That tests accessibility across a barrier, rather than proximity to it.

The protein tertiary structure is the overall spatial arrangement of one polypeptide chain. It includes how its protein secondary structures and intervening regions fit together. For example, the schematic under protein places positions 4 and 9 near each other despite their separation in protein primary structure. Such cooperation can help construct an active site; sequence distance and spatial separation answer different questions. Hydrophobicity, backbone hydrogen bonds and other interactions help stabilize folds, and some proteins additionally contain protein disulfide bonds. See Cooper: tertiary structure and interactions between chain regions.

Excess protein in urine. Glomerular disease, impaired renal tubule recovery and excess circulating small proteins produce different patterns; albuminuria names the albumin component.^[ref]

A molecular form of a protein defined by its amino-acid sequence and covalent modifications, including processing. Different conformations and mass-spectrometric charge states do not by themselves define different proteoforms.

A proteoglycan consists of a core protein bearing one or more covalently attached glycosaminoglycan chains. These chains are polysaccharides containing amino sugars. Thus the molecule combines a sequence-defined polypeptide with long carbohydrate components, whose number and composition can vary.^[ref]

An illuminating example comes from cartilage, where individual proteoglycans can associate with hyaluronic acid into larger aggregates. A proteoglycan molecule and an aggregate of many such molecules are different organizational levels: a change in aggregate size need not mean that every core protein has changed length.

In 1974, researchers digested bovine cartilage aggregates with enzymes and separated the resulting components by chromatography. They isolated a core-protein-derived fraction and a smaller linking-protein fraction that both retained binding to hyaluronic acid. Disassembly and selective recovery of binding components helped distinguish the carbohydrate-rich molecule from the interactions holding a larger aggregate together.^[ref]

A proteoliposome is a liposome containing one or more reconstituted membrane proteins in its lipid bilayer. It combines a controlled membrane boundary with a chosen molecular machine. A solution containing detergent-solubilized protein is not automatically a proteoliposome: a closed vesicle and a membrane-incorporated protein must actually be formed.

The artificial compartment is useful because material can be placed on one side of a lipid bilayer and transport measured across it. In an originating experiment on the NhaA sodium/proton antiporter, purified protein was reconstituted into sodium-loaded proteoliposomes. Parallel sodium and proton flux measurements, together with an independent membrane-potential equilibrium method, supported a stoichiometry of two protons per sodium ion over the tested pH range 7.2–8.1.^[ref]

For a bookkeeping example,100 sodium ions moved outward through a perfectly coupled $2{\mathrm{H}}^{+}/\mathrm{N}{\mathrm{a}}^{+}$ exchanger would accompany 200 protons moving inward. The net movement is 100 positive elementary charges inward, which explains the word electrogenic. These invented counts illustrate coupling, not a measured single-vesicle trace.

Interpreting a proteoliposome assay still requires knowing which way the membrane protein faces, whether the vesicles leak, and how much protein is incorporated. An otherwise matched empty liposome helps estimate membrane background. Reconstitution simplifies a biological system; it does not automatically eliminate every alternative source of the measured flux.

Proteolysis cleaves peptide bonds in proteins; it differs from reduction of protein disulfide bonds.