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The Biological Unit, also called the Biological Assembly, is the quaternary structure that is believed to be the functional form of a macromolecule. Often it is not the structure contained in the published PDB file, which is called the asymmetric unit. Therefore it is important to visualize the biological unit in order best to relate function to structure.
The Biological Unit, also called the Biological Assembly, is the quaternary structure of a protein that is believed to be the functional form of the molecule. It can be a single chain, or a quaternary assembly of multiple identical or non-identical chains. For example, the biological unit of hemoglobin includes two alpha chains and two beta chains, making it a tetrameric α2β2 structure. When a biological unit contains multiple chains that have co-evolved to bind to each other, it may also be referred to as a specific oligomer.
Of course, what is the functional form (biological unit) under one set of conditions may change under a different set of conditions, so there may be more than one functional form (biological unit) that includes a given protein chain. For example, phosphorylation or dephosphorylation by protein kinases or phosphatases often change the affinities between proteins, and hence their quaternary assemblies.
Published macromolecular structure data files (Atomic coordinate files, often in the PDB file format) contain the Asymmetric Unit, which may be identical with the biological unit, or only a portion of it, or may contain multiple biological units. Interchain contacts that occur in the asymmetric unit that are absent in the biological unit are termed crystal contacts. When publishing a macromolecular structure, the authors may elect to specify the biological unit. In the PDB file format, this is done in REMARK 350.
360 (virus capsid)
Truncated proteins may form oligomers that are impossible in the native protein. For example, 1bk5 (karyopherin alpha) is a truncated part of the natural chain, and forms a dimer that would be prevented by the full-length chain. Dimerization is dependent upon Y397. Mutation Y397D prevents this artifactual dimerization, leading to the monomer 1ee5.
How To Show The Biological Unit In Proteopedia
Please see Biological Unit: Showing.
Sources of Biological Unit Models
REMARK 350 in the PDB File Header
Biological units may be specified in REMARK 350 of the PDB file format. In some cases, more than one putative biological unit is specified, and downloadable from the Protein Data Bank. Biological units specified by the author(s) are distinguished from those predicted by software. An example is 3fad, which is explained in Looking at Structures: Introduction to Biological Assemblies and the PDB Archive.
The following servers generate biological unit models from REMARK 350:
- The MakeMultimer Server generates a PDB file in which every chain is assigned a distinct single-character name, and all chains are in a single model. MakeMultimer provides direct links for downloading, or for visualizing each biological unit in FirstGlance in Jmol.
- Atomic coordinates for biological units, when specified by the authors of a published structure in REMARK 350 of the PDB file format, are available from the RCSB (US) Protein Data Bank. As of April, 2010, "Biological Assemblies" were available at the bottom of the list under Download Files (upper right, near the large PDB code).
- One technical problem with the files from RCSB is that when they contain more than one copy of the asymmetric unit, the duplicated chains all have identical names. RCSB offers visualization of these models in Jmol, but it is usually difficult to tell how many chains are present in the biological unit, either in the snapshot (where each chain is colored similarly in a spectral amino- to carboxy-terminal sequence) or in Jmol, where coloring by chain fails to distinguish chains with the same name. Also, the additional copies are in separate models, which often complicates visualization. In contrast, coordinates for biological units available from MakeMultimer (see above), PISA or PQS (see below) are in a single model, and each chain is given a distinct name. RCSB also offers a viewer named Kiosk but this seems not to show the biological assembly.
As for author-specified biological assemblies, sometimes the specific oligomers were not known at the time the asymmetric unit was published. Also, some authors may have failed to specify the biological unit even when it was known. Rarely, the specified biological units might be incorrect. For all these reasons, it is advisable to consult other sources in addition to REMARK 350.
Protein Interfaces, Surfaces and Assemblies Server (PISA)
The Protein Interfaces, Surfaces and Assemblies Server (PISA) at the European Bioinformatics Institute uses improved methods to predict the biological unit or probable quaternary assembly, compared to its predecessor PQS (see next section). These servers examine the contacts that occur in macromolecular crystals used in X-ray crystallography. They attempt to discriminate between crystal contacts (artifacts of crystallization) and contacts between chains that have co-evolved to maintain specific oligomeric binding.
Probable Quaternary Structure Server (PQS)
The Probable Quaternary Structure Server (PQS) at the European Bioinformatics Institute examines the inter-chain contacts within protein crystals, and makes an educated guess (using published methods) about which contacts represent co-evolved specific oligomeric contacts, and which are artifacts of crystallization. It was usually correct, but not always. It returns models for what it deduces to be the biological units. There are many possible relationships between the asymmetric unit and the biological units returned by PQS. Examples are given in the discussion of PQS at ProteinExplorer.Org. Updates to PQS stopped in August, 2009. In 2010 it is being phased out in favor of PISA (see above).
- Biological Unit: Showing
- Crystal contacts
- X-ray crystallography
- Multi-protein assemblies
- Protein Interfaces, Surfaces and Assemblies Server (PISA) at the European Bioinformatics Institute.
- Probable Quaternary Structure Server (PQS) at the European Bioinformatics Institute.
- ProtBud, a database of biological unit structures Offers comparisons and downloads of the results from REMARK 350 vs. PQS.
- Biological Unit Tutorial at the RCSB PDB
- Biological Unit at PDBWiki
- COCOMAPS (bioCOmplexes COntact MAPS) is a web server for analysis and visualization of the interfaces present in biological complexes, such as protein-protein, protein-DNA and protein-RNA complexes, making use of intermolecular contact maps.
Literature citations will be found at the respective servers linked above.