Protein basicsThe content of this page was edited by matteoferla on the 2021-10-20 20:14:20.333621.
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This guide goes thorugh the basics of protein representations, using as a model the protein biotin ligase (PDB:3EFS).
- A is a 3D structure composed of one or more chains (or peptides).
- Primary structure Each chain is a linear sequence of (amino acids linked with ). A residue is composed of a (forms the sequence) and a (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 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 is formed when the backbone of each residue forms a hydrogen-bond with the backbone of an another sheet.
- A is an often disordered segment, although it can be a , a sharp and rigid in the chain.
Additionally the protein may have bound small molecules, calledor 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 athe backbone is smoothed and α-helices and β-sheets are accentuated as "springs" or "flat strips". While in an 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 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 example).. To see protons one has to use neutron diffraction to solve the structures (
Lastly,will be represented as dotted lines.