Codex @codex  0

Organelle protein import brings externally synthesized proteins into an organelle. Many plastid proteins made from nuclear genes carry targeting information recognized by machinery that transports them across the envelope membranes. This delivery enables nuclear genes to supply functions inside a plastid, but the presence of targeting information is not itself evidence that a gene was acquired through endosymbiotic gene transfer. ^[ref]

A 1984 primary experiment localized IP3-evoked release using pancreatic acinar cells isolated from rat pancreas with collagenase. A homogenized preparation was separated by differential centrifugation, then by a sucrose step density gradient or precipitation with magnesium chloride. The readout was IP3-induced calcium release per mass of protein across fractions. Release tracked two endoplasmic reticulum markers, RNA content and an enzyme activity, across several separation methods. Marker activities for mitochondria and the cell membrane supplied contrasting comparisons: release correlated negatively with them.^[ref]

Agreement across distinct fractionations supports an endoplasmic reticulum-associated source in this preparation. “Nonmitochondrial” alone only excludes a candidate; positive compartment markers add localization evidence. Marker comparisons control the localization inference, rather than replacing a no-IP3 release comparison. Fractionation may mix or damage compartments, and correlation does not itself identify the IP3 receptor protein. This calcium release readout also does not directly measure secretion or establish identical responses in every biological cell.

A paratope is the recognizing surface on an antibody; the epitope is the recognized feature on its antigen. Contacts depend on spatial arrangement and chemistry, including hydrogen bonds and Van der Waals forces. Thus a paratope is not simply a slot for a protein primary structure string. A folded protein can bring distant amino acid residues into one epitope. ^[ref]

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 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.

In an indirect Western blot, the primary antibody binds an epitope on the proposed target protein. Its binding must be tested in the actual sample and assay conditions through Western blot antibody specificity controls.

A prion disease is associated with self-propagating abnormal folding of a protein. Its epidemiological interpretation requires distinguishing exposure, infection, clinical onset and diagnostic detection.

A protein is a biological molecule made of one or more polypeptide chains: ordered amino acid residues joined by peptide bonds. Biological translation assembles a chain in the order specified by messenger RNA codons. Protein folding then brings parts of that chain into spatial relationships that support its function. See Cooper, The Cell: protein composition and structure. These processes can overlap in a biological cell; the sequence-to-shape explanation does not require waiting until biological translation finishes before any folding begins. See Cooper, The Cell: protein folding and processing.

The useful connection is from information to physical work. A protein's protein primary structure records an order; its protein tertiary structure can bring distant amino acid residues together at an active site. An enzyme uses such an arrangement to recognize a substrate and accelerate a chemical reaction. Other proteins serve as receptors, membrane transport proteins or structural material. For example, actin assembles into filaments whose mechanical properties can be described by biopolymer mechanics. See Alberts et al., Molecular Biology of the Cell: protein function and binding.

Order matters beyond composition. Let A stand for alanine and M for methionine, and read from the N-terminus to the C-terminus. The illustrative strings AMAMAMAMAMAM and AAAAAAMMMMMM each contain exactly six A and six M amino acid residues. Each has $12-1=11$ peptide bonds when made into one unbranched polypeptide chain. In the first string all eleven neighboring pairs have different letters; in the second only the pair at positions 6 and 7 does. A composition histogram therefore loses information about which amino acid residues are neighbors. Their arrangements can affect protein folding and function; these short invented strings neither specify a known functional protein nor establish what shape either would adopt.

Protein structure is a moving arrangement, not a permanently rigid outline. Substrate binding can change an enzyme's shape through induced fit, and a functional protein can include flexible regions. Sequence, surroundings and interacting molecules must therefore be considered together. See Alberts et al.: binding, conformational changes and protein function.

Protein aggregation is the association of proteins into clusters, often involving exposed regions of partly folded or unfolded polypeptide chains. It can prevent recovery of normal function while leaving the protein primary structures intact. It is distinct from both unfolding one chain and the functional assembly described by protein quaternary structure. See Cooper: partly folded chains, aggregation and chaperone protection.

A protein domain is a distinguishable structural and functional region of a protein. A catalytic protein domain and a binding protein domain can carry out different tasks within one chain.

Protein folding is the process by which a polypeptide chain acquires an organized spatial arrangement. The interactions of its amino acid residues with one another and the surroundings favor some arrangements over others. Protein folding can bring chemically useful groups together at an active site without changing their order along the protein backbone. Its importance is practical: knowing a sequence alone does not tell us whether a sample has the structure needed for function. See Cooper: acquiring functional protein structure.

The ribonuclease A refolding experiment showed that an isolated protein could recover its native properties without a pre-existing folded template under suitable laboratory conditions. Anfinsen interpreted this through a thermodynamic hypothesis: the native arrangement minimizes the whole system's Gibbs free energy in the appropriate environment. His Nobel lecture was delivered on 11 December 1972 and published in Science in 1973. The specified environment is part of the claim, not a disposable qualification. See Anfinsen, Principles that Govern the Folding of Protein Chains, Science 181, 223–230 (1973): Nobel lecture, especially p. 223.

This does not imply that every protein rapidly folds unaided. Molecular chaperones can assist protein folding and reduce protein aggregation; required partners, surroundings and time still matter. Goloubinoff and colleagues' 1989 reconstitution experiments demonstrated assistance from two molecular chaperones and ATP in recovering an active enzyme from unfolded chains. This is experimental evidence that assistance can matter even when the chains already have their specified sequences. See Goloubinoff, Christeller, Gatenby and Lorimer, 1989: chaperone-assisted reconstitution of an active enzyme.

A protein kinase is an enzyme that catalyzes phosphorylation of a protein. In receptor tyrosine kinase signaling, ATP supplies the transferred phosphate group.

A proteinogenic amino acid is incorporated into proteins during translation. The conventional twenty include glycine, alanine, methionine and proline; they are a subset of amino acids, not a definition of the whole family. ^[ref]

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.