Protein basics
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Proteins 101
This guide goes thorugh the basics of protein representations, using as a model the protein biotin ligase (PDB:3EFS).
- A protein is a 3D structure composed of one or more chains (or peptides).
- Primary structure Each chain is a linear sequence of residues (amino acids linked with peptide bonds). A residue is composed of a backbone (forms the sequence) and a side chain (stick out and differ for each type of amino acid).
- Secondary structure The chain is not straight, but folds into more energy-favourable conformations, mainly into
- An α-helix is a formed when the residues arrange themselves in a spring-like structure, where the backbone of each residue forms hydrogen bonds with the backbone of the residue 3-4 places ahead.
- A β-sheet is formed when the backbone of each residue forms a hydrogen-bond with the backbone of an another sheet.
- A loop is an often disordered segment, although it can be a , a sharp and rigid turn in the chain.
Additionally the protein may have bound small molecules, called ligands or prostetic groups. If they help to catalyse a reaction they are cofactors, if they are used in the reaction they are substrates.
There are various representation styles, in a ribbon/cartoon mode the backbone is smoothed and α-helices and β-sheets are accentuated as "springs" or "flat strips". While in an atomistic representation each element has a different colour, except carbon —white is hydrogen/proton, nitrogen is blue, oxygen is red, sulfur is yellow, phosphorous is orange and so forth. This molecule of ATP and biotin has five different colors.
In crystal structures one can find highly ordered water molecules, which, given that hydrogens are not visible by X-ray, will appear simply as a sphere. To see protons one has to use neutron diffraction to solve the structures (example).
Lastly, hydrogen bonds and other non-covalent interactions will be represented as dotted lines.