Protein structure prediction

Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes). Starting in 1994, the performance of current methods is assessed biannually in the CASP experiment (Critical Assessment of Techniques for Protein Structure Prediction). A continuous evaluation of protein structure prediction web servers is performed by the community project CAMEO3D. Proteins are chains of amino acids joined together by peptide bonds. Many conformations of this chain are possible due to the rotation of the main chain about the two torsion angles φ and ψ at the Cα atom (see figure). This conformational flexibility is responsible for differences in the three-dimensional structure of proteins. The peptide bonds in the chain are polar, i.e. they have separated positive and negative charges (partial charges) in the carbonyl group, which can act as hydrogen bond acceptor and in the NH group, which can act as hydrogen bond donor. These groups can therefore interact in the protein structure. Proteins consist mostly of 20 different types of L-α-amino acids (the proteinogenic amino acids). These 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 has the smallest side chain, only one hydrogen atom, and therefore can increase the local flexibility in the protein structure. Cysteine on the other hand can react with another cysteine residue to form one cystine 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.