Interresidue interactions in protein classes.
The free energy difference between folded and unfolded state is about the same for most proteins and it is not more than the energy of a few noncovalent interactions. In addition to the numerous noncovalent interactions, some proteins contain one or more disulfide bonds, which, as covalent crosslinks, significantly stabilize their tertiary structure. Correlation between the presence of disulfide bond(s), and the number noncovalent interresidue interactions of various kinds is analyzed here. The number of interactions per residue is almost the same for all protein. Also the number of long-range interactions per residue is the same in all proteins. Proteins with S--S bond(s) (extracellular proteins) have more medium-range and fewer short-range interactions than those without S--S bonds. However, the difference is independent of the number of these covalent crosslinks. We concluded that the different distributions of the various kinds of noncovalent interaction reflect the needs of proteins in the different environments, the extracellular and the intracellular ones, rather than the presence of the disulfide bond(s). We also pointed out that the observed differences in the distributions of short- and medium-range interactions are in good agreement with different secondary structure compositions of extracellular and intracellular proteins.
Gugolya
Z
Z
Department of Physics, University of Veszprém, Hungary.
Dosztányi
Z
Z
Simon
I
I
D000596:Amino Acids / Q000737:chemistry*; D016208:Databases, Factual; D004220:Disulfides / Q000737:chemistry; D016326:Extracellular Matrix Proteins / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D012984:Software
D000596:Amino Acids; D004220:Disulfides; D016326:Extracellular Matrix Proteins; D011506:Proteins