Other help topics:    For The Public

States Section

Introduction

The 'States' section of a Molecule Page provides a list of all known states of this molecule. A protein state is defined by the principal proteins interactions with other protein partners, covalent modifications on all protein components, association with small molecule ligands, and cellular location.

Clicking on a state name takes you to the detail page for the state. The state detail page shows a more detailed breakdown of the structure of the state, any functional annotations associated with this state, as well as any comments and citations entered by the author.

A "state description" entered by the author, is also displayed. This is given where a descriptive or commonly used name would be helpful to readers. The subcellular localization for each state is also given and a link to the transition graph is provided. Clicking on a transition graph icon (2 blue circles) provides a visual summary of other neighbouring states to and from which this state is directly converted.

Beneath the functional states may be a list of "class states". Some Molecule Page proteins have been assigned to a protein class (based on homology and functional similarity) in order to facilitate the creation of states. The use of protein classes permits an author to create all of these complexes at the same time and group them into a class state that represents the prototypical complex. For example, the notation (Gnb1|Gnb2|Gnb3) means that any of the three designated G protein beta subunits may be included in the state.

State Names and Signatures

For each state, there is a systematic "state name" that is computer-generated by the system based on the characteristics of the state. When you scroll over the state name with your mouse, the "state signature" appears in a yellow text box. The state signature is a unique identifier of the state that designates all the protein partners, covalent modifications, bound ligands, and cellular location. The state name is a working shorthand that is generated from the state signature.

To create an appropriately shortened state name from the state signature, we:

  1. Replace the protein name with gene symbols (e.g., Adenylyl cyclase type 2 becomes Adcy2)
  2. Designate covalent modifications with one- or two-letter abbreviations (e.g., P = phosphorylation, PA = palmitoylation) and remove information about the positions of covalent modifications. Therefore, Adenylyl cyclase type 2 that has been glycosylated becomes Adcy2 G
  3. Designate bound small-molecule ligands as numbered objects (e.g., L82 = GTP, L73 = GDP, L760 = forskolin etc.). Therefore, Adenylyl cyclase that has been glycosylated and has forskolin bound to it becomes Adcy2 G L760
  4. Display bound proteins/protein complexes with brackets around each interaction partner. Therefore, a state of G protein alpha s bound to a state of adenylyl cyclase type 2 becomes (Gnas 2PA L82) (Adcy2 G 2P).