Protein structure oligomeric

The surface traced out by the center of a solvent probe molecule as it is rolled over the surface of a protein whose three-dimensional structure has been determined at the atomic level. Solvent-accessible surface areas can be calculated by various computer algorithms, and differences in solvent-accessible areas can be used to characterize the energetics of surface hydration as a function of changes in protein conformation, oligomerization, and complexation. 

Mattinen, M.L., Heilman, M., Permi, P., Autio, K., Kalkkinen, N., Buchert, J. 2006. Effect of protein structure on laccase-catalysed protein oligomerization. J Agric Food Chem 54 8883-8890. 

Quaternary structure has advantages in potential for flexibility in function and regulation. This seems to be the main reason why so many proteins are oligomeric. It is now generally accepted that oligomeric proteins play a vital role in the overall mechanism of a cell. However, studies on the structural mechanisms by which they fulfill that role were not developed until recently because of the complexity of each oligomeric protein. As described above, recent results have provided valuable insights on the structure-function... 

Cellular and viral IL-lOs and IFN-7 form intercalated dimers (Fig. 2). The intercalated dimer is formed from the first four secondary structural elements from one chain (A-D) and the final two (E and F) from the other. The intertwined dimer fold observed for IFN-7, IL-10, and many other protein structures, is proposed to be an evolutionary mechanism of protein oligomerization referred to as 3D domain swapping (Bennett et at., 1995). This theory suggests IFN-7 and lL-10 evolved from a monomeric protein by exchanging structural domains (a-helices E and E) with another monomer to create the dimer. This hypothesis is strengthened by the discovery of the monomeric IL-lOFMs, lL-19, IL-20, and IL-22. In fact, the close relationship between the intertwined dimeric IFN-7 and monomeric type 1 IFNs was clearly identified when the first structure of IEN-7 was completed in 1991 (Ealick et at, 1991). 

In some cases proteins are divided into two or more domains (Fig. 1), each of which is like a globular protein but connected covalently to other domain(s) by the continuous polypeptide chain. Other proteins are oligomeric in that they are composed of several unconnected polypeptide chains (subunits) that usually, but not always, fold up independently and assemble to form the complete protein. The arrangement of the subunits relative to each other is referred to as the quaternary structure. Hemoglobin (a202) (Fig. 6) and aspartate transcarbamoylase (a6/36), where a and j3 refer to different types of subunits, are well-studied cases where different quaternary structures occur with significantly altered properties. 

Popot JL (1993) Integral membrane protein structure Transmembrane alpha-helices as autonomous folding domains. Curr Opin Struct Biol 3 532-540 Popot JL and Engelman DM (1990) Membrane protein folding and oligomerization The two-stage model. Biochemistry 29 4031-4037... 

ERRAT contains a database of acceptable nonbonded atom-atom distances. It classifies the atom-atom distances in a proposed structure and then does a statistical evaluation of those atom-atom distance interactions. The parameters used to construct the database were derived from known protein structures of varying fold classifications. The known structures used for the database were required to have a maximum resolution of 2.5 A, an R-factor less than 25%, be monomeric or homo-oligomeric, be native structures, and contain peptide bond dihedral angles 15° from ideal values based on the secondary structure. A total of 96 solved X-ray protein structures from the PDB were used as the dataset of correct protein structures. The six types of atom-atom distances were restricted to be atoms from different amino acid residues or to be atoms that interact with each other with a through-space distance no greater than 3.5 The average and standard deviation of each atom-atom distance interaction fraction (the fraction of specific atom-atom pairwise distances in a protein structure), as illustrated in Eq. [4] for CC distances... 

A possible hierarchy of protein folding corresponding to the hierarchy in protein structure was suggested (Schulz, 1977). It can be summarized by the following scheme for folding in stages with an additional level for oligomeric proteins, the subunit assembly ... 

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