Biological Unit

From Proteopedia

Jump to: navigation, search

The Biological Unit, also called the Biological Assembly[1][2], is the quaternary structure that is believed to be the major 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.

Contents

Definition

The Biological Unit, also called the Biological Assembly[1][2], is the quaternary structure of a protein that is believed to be the main 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, 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.

Examples

Model

Chains in
asymmetric unit

Chains in
biological unit

1b6b
3vpa
12e8
3dxa

2
4
4
15

1
1
2
5

4mdh
3dxk

2
7

2
7

5cev

6

6*

1qrd

2

2* **

3m6y

4

4**, 4*, 2, 2

3dxp
1hho
3dxr

1
2
2

2
4
6, 12

1sva

6

360 (virus capsid)


 * The contacts in this biological unit differ from those in the asymmetric unit.

 **The "author specified" assembly (in this case the same as the asymmetric unit) appears unlikely in view of the assembly predicted by PISA, which has a much larger buried surface area.

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.


Visualizing the Biological Unit

Proteopedia

On pages titled with a PDB code, Proteopedia shows biological unit 1 by default, with an option to show the asymmetric unit instead. A simple example is 3hyd: biological unit 1 has 4 small peptide chains, while the asymmetric unit has a single chain. A large example is 1pov, the polio virus capsid. When biological unit 1 becomes too large for JSmol to handle effectively, it is displayed in Mol* ("Molstar") instead of JSmol. An example is the much larger capsid of Eastern Equine Encephalitis Virus, 6mx4.

FirstGlance in Jmol

FirstGlance in Jmol makes it quick and easy to see, explore, and analyze the biological unit. The initial display in FirstGlance is automatically "biomolecule 1" from REMARK 350. When it is very large, it will be simplified to alpha carbon atoms (or a subset thereof) automatically by FirstGlance.

  • Display the molecule in FirstGlance in Jmol:
    • Enter the PDB code in the top search slot at the left edge of any page in Proteopedia. At the page in Proteopedia titled with the PDB code, under Resources, click on the link to FirstGlance.
    • Alternatively, go directly to http://FirstGlance.Jmol.Org (not https) and enter the PDB code.
  • In the Molecule Information tab (the first/left-most tab), click Biological Unit and follow instructions. When there is more than one biological unit, all will be listed and you can display and analyze each of them.

How To Show The Biological Unit In Proteopedia

Please see Biological Unit: Showing.

Unreliability of REMARK 350 in the PDB File Header

When a structure is deposited in the PDB, the authors are required to specify the biological unit if it is known. This is given in REMARK 350 in the header of the PDB file format. Unfortunately, information in REMARK 350 is often incorrect (see discussion of this problem by Roland Dunbrack)[1][2]. There are numerous examples in which the authors state that the biological unit is a monomer in REMARK 350, but provide good experimental evidence in the paper reporting the structure that the biological unit is a dimer. Jose Duarte provided a list of examples.

In 2022, the wwPDB is adding REMARK 350 to PDB-format files originally deposited without that remark, mostly models determined by NMR. What is unfortunate is that the added REMARK 350 specifies "AUTHOR DETERMINED", although it appears that the authors are not being consulted about whether the deposited model is believed to be the biological unit (major functional assembly). An example is 2z59 deposited in 2007 and released in 2008, which lacked REMARK 350 until it was added on March 16, 2022 (see the REVDAT records in the PDB format file).

In some cases, more than one putative biological unit is specified in REMARK 350. Biological units specified by the author(s) are distinguished from those predicted by software. An example is 3fad, which is explained in Introduction to Biological Assemblies and the PDB Archive.

The most reliable way to find out the biological unit is to read the literature and/or contact experts on the molecule in question. Short of such efforts, here are some suggestions:

  • When the "author determined" biological unit stated in REMARK 350 has a different number of chains than the asymmetric unit, the biological unit is more likely to be correct, simply because the difference in chains shows that the authors gave REMARK 350 some real consideration.
  • When the "author determined" biological unit stated in REMARK 350 has the same number of chains, but in a different conformation, than the asymmetric unit, the stated biological unit is more likely to be correct, for the same reason given in the previous case above. An example is 1qrd, given in the table in the Examples section above.
  • When the "author determined" biological unit stated in REMARK 350 has the same number of chains, in the same conformation, as the asymmetric unit, the stated biological unit is less likely to be correct. There is a significant chance that the authors failed to state a known biological unit in REMARK 350 (see examples above).
  • When a biological unit is determined only by software, it is less likely to be correct. The software makes an educated guess based upon the characteristics of the contacts present in the protein crystal, but it is sometimes incorrect.

Generation of Biological Unit Models from REMARK 350

The following sources generate biological unit models from REMARK 350. Be aware that, as explained above, REMARK 350 may be incorrect.

FirstGlance in Jmol Limitation

FirstGlance automatically displays biological unit 1, and enables you to work with it using all of the tools within FirstGlance. However, you cannot save the biological unit model in PDB format, because internally JSmol assigns multiple-character names to duplicated chains. For example, with 3hyd, chain A is duplicated to chains A1, A2, A3. These chain names render the pseudo PDB file saved from FirstGlance/JSmol unreadable for many software packages.

MakeMultimer

  • The MakeMultimer server by Michael Palmer (University of Waterloo, Ontario, Canada) served FirstGlance well from May, 2010, until late 2021, when it was retired. It generated a PDB file in which every chain is assigned a distinct single-character name, and all chains are in a single model. FirstGlance 4.0, released August 15, 2022, was designed to make external generation of a biological unit PDB file unnecessary.

RCSB

  • 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 PISA (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.

Software: 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. It examines the contacts that occur in macromolecular crystals used in X-ray crystallography. It attempts to discriminate between crystal contacts (artifacts of crystallization) and contacts between chains that have co-evolved to maintain specific oligomeric binding.

Software: Evolutionary Protein-Protein Interface Classifier (EPPIC)

The Evolutionary Protein Protein Interface Classifier Server (EPPIC) classifies all protein-protein contacts in crystal lattices as biologically relevant or crystal contacts and provides an assessment of how the biologically relevant interfaces combine into a biological assembly. EPPIC takes a fundamentally different approach than PISA, and it should be seen as complementary to PISA. The authors suggest combining with PISA to improve biological assembly assignments.

Software: The Protein Common Assembly Database (ProtCAD)

The Protein Common Assembly Database (ProtCAD) is a database of protein complexes based on structures observed in independent experimental structure determinations of the same or homologous proteins in the Protein Data Bank, with the occurrence in multiple experiments providing validation.


See Also

Web Sites

Literature Citations

Literature citations will be found at the respective servers linked above.

  1. ↑ 1.0 1.1 1.2 Freely available preprint of Xu and Dunbrack's 2019 "Principles and characteristics of biological assemblies in experimentally determined protein structures".
  2. ↑ 2.0 2.1 2.2 Xu Q, Dunbrack RL Jr. Principles and characteristics of biological assemblies in experimentally determined protein structures. Curr Opin Struct Biol. 2019 Apr;55:34-49. doi: 10.1016/j.sbi.2019.03.006. Epub, 2019 Apr 6. PMID:30965224 doi:http://dx.doi.org/10.1016/j.sbi.2019.03.006

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, Eran Hodis, Jaime Prilusky

Retrieved from "http://proteopedia.org/wiki/index.php/Biological_Unit"
Personal tools