A 3-10 helix repeats carbonyl-i to NH-(i+3) hydrogen bonds and has about three residues per turn. The “10” counts atoms in its hydrogen-bonded ring.

A pi helix contains carbonyl-i to NH-(i+5) hydrogen bonds, sixteen-membered hydrogen-bonded rings, and approximately 4.4 residues per turn.

A protein complex is an assembly of associated proteins. Its composition specifies component identities and their stoichiometry; variable accessory occupancy and transient partners can make the assembly a molecular population of related forms rather than one fixed object.

A protein sequence records the order of amino acid residues in a polypeptide chain. The sequence alone does not specify every modification, covalent crosslink, assembly state or conformation present in a purified sample.

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 clade-A Arabidopsis phosphatase that negatively regulates ABA responses, including kinase activation in guard cells.

An assembly containing two protein subunits. A binding unit in an assay need not be a single polypeptide chain.

N-linked glycosylation attaches a glycan through a nitrogen atom, commonly the side-chain amide nitrogen of asparagine. In the ER pathway, an assembled lipid-linked oligosaccharide is transferred to an appropriate protein acceptor.

O-linked glycosylation attaches a sugar through an oxygen atom on the acceptor, often a protein hydroxyl group. Several different pathways and donor specificities fall under this description.

The predominantly alpha-helical structural framework characteristic of globins. Conserved haem-pocket architecture in myoglobin and haemoglobin supplies evidence for divergence from a shared ancestor.

A model-based measure of the amplitude of internal bond-vector motion inferred from suitable relaxation measurements. It requires assumptions about overall tumbling and timescale separation.

The distribution of molecular conformations and their interconversion in an enzyme under specified chemical conditions. A minor conformational population can be functionally important even when a mean structure changes little.

A protein domain that can recognize particular methylated histone states, with specificity depending on the particular protein.

A DNA-binding domain is a region of a protein contributing to DNA recognition or binding. Its binding specificity can be separable from an activation domain, allowing experimental tests of recognition and transcriptional stimulation.

An activation domain is a protein region that promotes transcription when appropriately recruited, often through enzyme cofactor interactions. Tethering experiments can distinguish activation capacity from the sequence specificity supplied by a DNA-binding domain.

A helix-turn-helix is a structural DNA-binding motif in which an intervening turn relates two helices, one often contributing major-groove recognition contacts. The motif alone does not specify which DNA sequence is recognized.

A carbohydrate-binding module targets an associated protein to a carbohydrate substrate. Surface enrichment can help insoluble-substrate catalysis, but binding alone does not establish productive access.

Domain shuffling creates new protein architectures by combining domains in new arrangements during evolution. A binding domain joined to a catalytic domain can bring an existing chemistry to a new substrate or location. The domains need not retain identical behaviour after recombination because interfaces, linkers and regulation can change. Comparing domain arrangements therefore complements whole-sequence similarity when reconstructing functional evolution. ^[ref]

A DNA-binding protein domain encoded by a homeobox, typically about 60 amino acids long.

Its folded structure presents a DNA-recognition surface and supports sequence-selective regulation. A homeobox is the corresponding DNA sequence category; a homeodomain is part of the encoded protein, so the terms refer to different molecular objects. ^[ref]

A protein structural motif stabilized by zinc coordination. Different zinc-finger families can bind DNA, RNA or proteins; the motif alone does not establish a transcriptional role.