Crystal contacts

From Proteopedia

Crystal contacts are the contacts that occur between molecules in crystals of macromolecules. These contacts are what hold the crystal together. The term crystal contacts is usually used to refer to intermolecular or interchain contacts that occur only in a crystal, and not when the molecule is in its native functional state. Thus, crystal contacts, in this narrower sense, are an artifact of crystallization.

In contrast, contacts between chains that occur in the native functional state of the molecule are called specific oligomeric contacts. The resulting functional quaternary structure is called the biological unit or biological assembly. Specific oligomeric contacts occur through interfaces that have co-evolved to fit together and bind under the proper circumstances. Some molecules have multiple quaternary forms. For example, protein phosphorylation often controls the affinities of partner chains for each other.

Crystal contacts tend to be smaller and to involve more hydrophilic surfaces, in contrast to specific oligomeric contacts which are larger and may bury some hydrophobic surface^{[1] [2]} . These differences are used to predict which contacts occuring in a given protein crystal are crystal contacts and which are specific oligomeric contacts^{[3] [4] [5]}. An early server with a high success rate at predicting quaternary structures was the Probable Quaternary Structure Server (PQS)^[6] at the European Bioinformatics Institute. No further updates with new structures have been done at PQS since August, 2009, and it is being phased out in 2010 in favor of a newer server, Protein Interfaces, Surfaces and Assemblies (PISA).

See Also

• Biological unit which includes examples of crystal contacts.
• X-ray crystallography
• Crystal Contacts at Protein Explorer, with snapshots of examples.

References

1. ↑ Dasgupta S, Iyer GH, Bryant SH, Lawrence CE, Bell JA. Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins. 1997 Aug;28(4):494-514. PMID:9261866
2. ↑ Janin J. Specific versus non-specific contacts in protein crystals. Nat Struct Biol. 1997 Dec;4(12):973-4. PMID:9406542
3. ↑ Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci. 1998 Sep;23(9):358-61. PMID:9787643
4. ↑ Ponstingl H, Henrick K, Thornton JM. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins. 2000 Oct 1;41(1):47-57. PMID:10944393
5. ↑ Ponstingl H, Kabir T, Gorse D, Thornton JM. Morphological aspects of oligomeric protein structures. Prog Biophys Mol Biol. 2005 Sep;89(1):9-35. PMID:15895504
6. ↑ Ponstingl H, Henrick K, Thornton JM. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins. 2000 Oct 1;41(1):47-57. PMID:10944393