Protein Structure Prediction - Protein Structure and Terminology

Protein Structure and Terminology

Proteins are chains of amino acids joined together by peptide bonds. Many conformations of this chain are possible due to the rotation of the chain about each Cα atom. It is these informational changes that are responsible for differences in the three dimensional structure of proteins. Each amino acid in the chain is polar, i.e. it has separated positive and negative charged regions with a free C=O group, which can act as hydrogen bond acceptor and an NH group, which can act as hydrogen bond donor. These groups can therefore interact in the protein structure. The 20 amino acids can be classified according to the chemistry of the side chain which also plays an important structural role. Glycine takes on a special position, as it does not have a side chain and therefore can increase the local flexibility in the protein structure. Cysteine on the other hand can react with another cysteine residue and thereby form a cross link stabilizing the whole structure.

The protein structure can be considered as a sequence of secondary structure elements, such as α helices and β sheets, which together constitute the overall three-dimensional configuration of the protein chain. In these secondary structures regular patterns of H bonds are formed between neighboring amino acids, and the amino acids have similar Φ and Ψ angles.

The formation of these structures neutralizes the polar groups on each amino acid. The secondary structures are tightly packed in the protein core in a hydrophobic environment. Each amino acid side group has a limited volume to occupy and a limited number of possible interactions with other near- by side chains, a situation that must be taken into account in molecular modeling and alignments.