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Concepts
Proteins interact chemically by participating in chemical reactions. Multiple molecules including proteins can be reactants or products of chemical reactions. They can catalize, inhibit or regulate them.
They also contribute to the adition or removal of small chemical groups to certain residues (amino acid) in the peptide chain. For example, the addicion of a phosphate group to a certain amino acid side chain of a protein.
Other types of interactions among proteins are physical like the formation of complexes, where multiple proteins get together forming a bigger molecule.
Term to designate all of the different molecular forms in which the protein product of a single gene can be found, including changes due to genetic variations, alternatively spliced RNA transcripts and post-translational modifications[1].
Biological network formed by nodes and links, where the nodes are proteoforms and the links are connections between the proteoforms. The connections can represent interactions like binding or other covalent modifications like addition or removal of molecular groups at a position in the peptide sequence of the protein.
Proteoform networks can have the form of interaction networks, but also of pathway networks where more details are shown instead if limiting to simple undirectional connections among pairs. There can be multiple types of links like catalysis or inhubition of activity in other proteoforms.
The number of connections of a node. In other words, the number of direct neighbours of a node in the network.
Node with a very high degree in comparison with the rest of the nodes in the network.
Situation when the shortest path between the majority of the nodes in a network is very small due to the high degree of some fraction of the nodes[2].
[1] Smith, L. M. et al. Proteoform: a single term describing protein complexity. Nature Methods 10, 186, doi:10.1038/nmeth.2369 (2013).
[2] Travers, J., & Milgram, S. (1969). An Experimental Study of the Small World Problem. Sociometry, 32(4), 425-443. doi:10.2307/2786545