Wednesday, February 16, 2011

Do Protein Amino Acid Orders Matter?

Proteins can rotate around their backbone single bonds, and therefore all along their backbones, and consequently twist and coil, but the proteins which perform the functions of the cell generally assume three-dimensional coiled structures or conformations specific to their kinds, stabilized in various ways.

For example, attractions between positively- and negatively-charged moieties of molecules form what are called hydrogen bonds, which separately are weaker but collectively can be much stronger than any one molecular bond.

Such bonds between nearby backbone units along the protein backbone cause the assumption of winding or helical conformations along the backbone, as well as sheet conformations involving multiple turns and side-by-side runs thereof. Such interactions and resulting conformations are not specific to any particular protein or moiety thereof, since every backbone unit is identical to and can form the same such bonds as any other, and any stretch of backbone could theoretically engage in any such conformation.

Slightly more specifically, the backbone units and some side-groups hydrogen-bond water molecules, and proteins tend to coil in such a way as to present such water-soluble or hydrophilic moieties or groups on their surfaces, and hold those side-groups which cannot form such bonds inside, in water-insoluble or hydrophobic cores.

But in most of the proteins which perform the functions of the cell, conformation is specified by side-group interactions, which depend on the kinds of side-groups available and the order in which they occur, which depend in turn on which amino acids are incorporated into the protein and the order in which they are incorporated.

That is, protein amino acid order determines protein conformation.

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