Codex @codex  0

An amino acid combines carboxylic acid and amine functionality in the same molecule; the name alone does not specify their separation. An alpha-amino acid has its amino nitrogen attached to the carbon immediately adjacent to the carboxyl carbon, the amino acid alpha carbon. For example, ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ is glycine, whereas ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ has an extra intervening carbon and is not an alpha-amino acid. These chemical formulas describe connectivity, not the predominant protonation state in water.

Most common proteinogenic amino acids share the skeleton ${\mathrm{H}}_2\mathrm{N}-\mathrm{CH}(R)-\mathrm{COOH}$, with $R$ the amino acid side chain. In glycine, $R$ is hydrogen; in alanine, $R=\mathrm{C}{\mathrm{H}}_3$. Proline is a useful exception to the displayed primary-amine skeleton: its amino nitrogen is part of a ring and has a second carbon substituent. The shared backbone permits assembly into polypeptides, while different amino acid side chains give the resulting proteins diverse chemistry. ^[ref]

In a chemical solution, protonation changes the electric charges without changing this backbone. Free glycine near neutral pH is predominantly ${\mathrm{H}}_3{\mathrm{N}}^{+}-\mathrm{C}{\mathrm{H}}_2-\mathrm{CO}{\mathrm{O}}^{-}$, a zwitterion. Its positive and negative groups are joined within one molecule; zero net electric charge does not mean absence of local electric charges, nor does it mean the uncharged drawing ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ predominates. Glycine protonation explains how lowering or raising pH changes the balance. ^[ref]

Building a protein joins the carboxyl carbon of one amino acid to the amino nitrogen of another through a peptide bond, an amide linkage. The formal net condensation loses the elements of water; cellular translation uses activated substrates at a ribosome, rather than simply mixing free amino acids in water. Incorporated units are amino acid residues. The interior amide groups no longer have the same acid/base behavior as the two free terminal groups of glycine, so its free-molecule glycine titration cannot be copied independently at every chain position. ^[ref]

Chirality distinguishes most common proteinogenic amino acids from glycine. The other nineteen members of the conventional twenty have a stereocenter at their amino acid alpha carbon; ordinary translation incorporates their L forms. Glycine's two identical hydrogen substituents make it achiral. Thus being an amino acid, or even an alpha-amino acid, does not by itself imply chirality. ^[ref]

Molecular biologist studying transport of proteins across membranes. With Günter Blobel, Dobberstein reconstructed steps of the secretory pathway, connecting information in a nascent polypeptide with membrane-associated targeting.^[ref]

B. W. Poovaiah is a researcher in plant signal transduction, particularly the roles of calcium ions and calmodulin. His laboratory's research connects these intracellular signals to plant growth and responses to other organisms.^[ref]

With K. Veluthambi, B. W. Poovaiah investigated how auxin affects developing strawberries. Removing the surface achenes stopped growth and altered the pattern of polypeptides detected by SDS-PAGE. Applying the synthetic auxin naphthaleneacetic acid restored growth and the appearance of several development-associated polypeptides.^[ref]

The experiment illustrates a useful strategy for investigating a biological signal: remove its normal source, then ask whether supplying a candidate signal restores the response. Recovery of both growth and a molecular readout makes the proposed connection more informative than a simple correlation between fruit size and protein abundance. The SDS-PAGE bands report molecular changes; their appearance alone does not identify each protein's function.

Carissa L. White coauthored a 2002 study identifying a heparosan synthase. The characterized glycosyltransferase combined two sugar-transfer activities in one protein, building a heparosan chain from glucuronic acid and N-acetylglucosamine units. The product was the unsulfated, unepimerized backbone related to heparin, rather than a fully modified heparin molecule.^[ref]

The study tested which nucleotide sugars supported chain formation and compared the product's susceptibility to different polysaccharide-cleaving enzymes. An illuminating distinction is between building a repeating backbone and modifying that backbone: identifying a heparosan synthase establishes a particular polymerization activity, but does not establish all the later reactions needed to make a differently substituted glycosaminoglycan. The reported one-protein, two-activity mechanism also shows that two alternating chemical additions need not require two separate polypeptides.^[ref]

A coding sequence is the part of a nucleotide sequence that specifies a polypeptide through the genetic code. In a processed eukaryotic transcript it excludes untranslated regions; a genomic region may require removal of introns before bacterial expression.

Collagen IV, also called type IV collagen, is the network-forming collagen that provides a major scaffold of basement membranes. Three polypeptide chains assemble into a molecular unit, and units associate through their ends into a sheet-like network. This organization suits a thin supporting layer beneath an epithelium, rather than a long cable made of parallel molecules.^[ref]

The Collagen IV NC1 domain is a noncollagenous end region where adjoining molecular units meet. A sulfilimine bond links a methionine side chain in one unit to a hydroxylysine side chain in another. Thus the scaffold combines molecular association with a chemically specific covalent bond.^[ref]

One can distinguish two questions about a basement membrane: which proteins form its scaffold, and how neighboring units are fastened together. Isolating linked peptides and comparing their mass spectrometry and nuclear magnetic resonance signals answered the second question. The investigation connected a tissue-scale network to the identities of individual amino acid residues.^[ref]

A Collagen IV NC1 hexamer is a six-subunit junction formed when the C-terminus ends of two Collagen IV protomers associate. Each three-chain protomer contributes three Collagen IV NC1 domains. The resulting arrangement is therefore two three-subunit ends joined together, one local connection in a basement membrane scaffold.^[ref]

Up to six sulfilimine bonds can reinforce the interface between the two ends. Analysis of linked peptides by mass spectrometry and nuclear magnetic resonance, followed by chemical reduction that separated the linked components, established the chemistry of this reinforcement.^[ref]

This provides a useful distinction between subunit counting and bond counting. Six subunits describes the intact junction's architecture; the number of reinforcing links is another property. Neither number implies that a single Collagen IV protomer has six polypeptide chains.

A Collagen IV protomer is a three-chain molecular unit of Collagen IV that assembles with other units to form a basement membrane network. Much of its length has a collagen triple helix, while its C-terminus presents three Collagen IV NC1 domains. Association of two such ends forms a Collagen IV NC1 hexamer.^[ref]

The organizational levels can be counted separately. Ten intact three-chain Collagen IV protomers contain thirty polypeptide chains, but this count does not describe how the ten units are connected. A six-subunit NC1 junction joins two protomers at one end; it does not convert either protomer into a six-chain molecule.

The term is therefore useful when moving between a protein's molecular composition and the architecture of the scaffold it builds. Identifying a three-chain unit answers a different question from identifying the contacts and covalent bonds between neighbouring units.

A collagen triple helix is a protein structure in which three polypeptide chains wind together into a right-handed superhelix; each individual chain has a left-handed, polyproline-II-like conformation. It is characteristic of collagen and differs from a single alpha helix. The close-packed structure connects protein primary structure to a three-chain assembly: glycine commonly occurs at every third residue in the triple-helical region, conventionally written Gly–X–Y.^[ref][ref]

Glycine's small side group permits close approach near the central axis. Proline and hydroxyproline are frequent at the other positions, while interchain hydrogen bonds and interactions with water help organize the assembly. A model segment with ten Gly–X–Y repeats has 30 residues per chain and 90 across three chains; the three-chain count is distinct from the three-residue sequence period.

The structural picture developed from fiber-diffraction constraints in work by G. N. Ramachandran, G. Kartha and other investigators, rather than from directly seeing every atom in an intact tissue. Later, a synthetic collagen-like peptide provided a sharper test. Its 1994 X-ray crystallography structure, reported at $1.9$ angstrom resolution, confirmed triple-helical packing and interchain bonding. A deliberately introduced glycine-to-alanine substitution caused local untwisting and replaced direct interchain contacts near the substitution with water-mediated bridges.^[ref]

The experiment illustrates why sequence changes can affect a material: even a small side-group change can disturb local packing. The triple-helical molecule is one level of organization; the larger collagen fiber includes additional assembly beyond these three chains.

Corticosteroid-binding globulin is a plasma protein that binds cortisol and carries it in the blood. It is a glycoprotein: carbohydrate groups are attached to its polypeptide chain. Binding creates a circulating hormone pool whose behaviour depends on the state of the carrier, as well as on the amount of cortisol present.^[ref]

In a 1990 experiment, neutrophil elastase cleaved corticosteroid-binding globulin near its C-terminus. More than 80% of the bound cortisol was released under the assay conditions. The carrier did not inhibit the enzyme; it served as a substrate. This linked a chemically specific cleavage to a change in hormone binding.^[ref]

The experiment illustrates why total hormone and freely dissolved hormone are different quantities. A change in carrier binding can redistribute an existing hormone pool without requiring immediate synthesis of additional cortisol. The percentage released in this assay is not a universal release fraction for every tissue or physiological condition.

C. Ramakrishnan helped investigate the geometry of polypeptide chains through backbone torsion angles. Steric restrictions rule out some angle combinations, providing a structural constraint that a protein model must satisfy in addition to its sequence.^[ref]

Cell biologist who, with Günter Blobel, used controlled digestion of nascent polypeptides to investigate their location in cellular fractions. Protection from digestion connected membrane enclosure with the path of protein synthesis.^[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]

G. Kartha worked with G. N. Ramachandran on the structure of collagen. Their 1955 paper developed a model in which three polypeptide chains wind around one another, contributing to the explanation of the collagen triple helix. The proposed arrangement had to accommodate the amino acid composition, hydrogen bonding and the pattern of experimental X-ray diffraction.^[ref]

The history illustrates how a structural model is tested. A geometrically plausible arrangement can still require revision if its predicted repeat disagrees with measured X-ray diffraction. The value of the model lies in connecting molecular packing with several independent observations, while leaving its detailed geometry open to correction. A proposed protein structure and a later experimentally refined atomic structure represent different stages of that process.^[ref]

Glucagon is a peptide hormone made by alpha cells in the pancreatic islets. Its mature polypeptide has 29 amino acid residues. Alpha cells store glucagon in secretory granules and release it by exocytosis. Glucagon is a message about fuel availability; glucose is the sugar whose supply it helps regulate. A falling blood glucose concentration favors glucagon release, whereas a rise usually suppresses it. Amino acids can also stimulate release, so a meal containing protein need not produce the same hormone pattern as a meal dominated by carbohydrates. ^[ref]

The principal blood glucose-raising target is the liver. In a hepatocyte, the glucagon receptor is a G protein-coupled receptor: activation of a stimulatory G protein drives adenylyl cyclase, increasing the second messenger cAMP and activating protein kinase A. Downstream phosphorylation, including the phosphorylase kinase relay to glycogen phosphorylase, favors glycogenolysis. Glucagon also supports gluconeogenesis. These are different supplies: glycogenolysis draws on a finite glycogen reserve, whereas gluconeogenesis makes glucose from other substrates and depends on their availability. Longer fasting depletes the glycogen reserve; a stronger hormone signal cannot release material that is no longer there. ^{[ref] [ref]}

Do not copy the liver pathway into every target of insulin. Skeletal muscle uses its own glycogen reserve locally; its glucose uptake and the liver's glucose output are different flows. Nor is direct glucagon-stimulated lipolysis in human adipose tissue as firmly established as its action in the liver. Glucagon action depends on the tissue, other hormones, and available substrates. ^[ref]

There is a useful surprise inside the pancreatic islets: local glucagon can support insulin release from neighboring beta cells. The islet perifusion experiment distinguishes that interaction from glucagon's action on the liver. Thus the two hormones can oppose each other's effects on blood glucose while cooperating locally. Delta cells supply another local brake through somatostatin. ^{[ref] [ref]}

A glutamate unit in a polypeptide. An appropriately positioned carboxyl group can participate in proton transfer and substrate or water positioning.

A glutamic acid residue is an amino acid residue represented by Glu or E in polypeptide sequence notation. GAA and GAG specify glutamic acid residues in the standard genetic code; the ribosome example uses GAA as its third codon. See Elzanowski and Ostell, NCBI: standard genetic code, table 1. The name denotes an incorporated chain position, as distinguished from a free amino acid molecule.

Cell biologist studying protein targeting across membranes. With Bernhard Dobberstein, Blobel reconstructed aspects of cotranslational protein translocation, connecting information in a growing polypeptide with delivery to the secretory pathway.^[ref]

A histidine unit within a polypeptide.

A homodimer is a protein complex containing two copies of the same protein subunit type, conventionally written $A_2$. A heterodimer instead contains two different types, $AB$. Identical subunit type does not require the copies to occupy identical conformations or environments in every instant of the complex's motion.

Assembly is part of protein quaternary structure, rather than a claim that the two chains have become one longer polypeptide. If each subunit contains 100 amino acid residues, the homodimer contains 200 residues across two chains. Association alone need not add a peptide bond between them.

For reversible association $2A\rightleftharpoons A_2$, a concentration-form dissociation constant isThe second equation counts subunit equivalents. For $[A]=2\mu \mathrm{M}$ and $[A_2]=1\mu \mathrm{M}$, $C_{\mathrm{total}}=4\mu \mathrm{M}$: half the subunit copies reside in dimers, even though dimers comprise only one third of the separate molecular particles. The written $K_d$ uses the usual macroscopic concentration convention.

HIV-1 protease supplies an experimentally important example. Recombinant enzyme had reported molecular masses of approximately 11,000 under denaturing conditions and 22,000 under nondenaturing conditions; chemical crosslinking provided additional evidence consistent with an active two-subunit enzyme. Comparing several measurements was more informative than assigning a homodimer solely from an apparent mass in one assay.^[ref]