Protein (source code)
= Protein
{wiki}
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 https://www.ncbi.nlm.nih.gov/books/NBK9879/[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 https://www.ncbi.nlm.nih.gov/books/NBK9843/[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 https://www.ncbi.nlm.nih.gov/books/NBK26911/[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.
\Image[/protein-sequence-to-fold.png]
{title=From <amino acid> order to an imagined fold and binding site}
{description=Original schematic using two twelve-residue strings with equal composition. The imagined fold uses the first string: colors and numbers preserve its <protein primary structure>, while positions 4 and 9 approach one another. The binding-site cartoon explains spatial cooperation, not an actual <enzyme> or a measured <protein structure>. No actual coordinates, physical scale or exact <protein folding> predictor are implied.}
<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 https://www.ncbi.nlm.nih.gov/books/NBK26911/[Alberts et al.: binding, conformational changes and protein function].
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