Structure to function

Protein structural models are usually obtained by two experimental methods, X-ray crystallography and nuclear magnetic resonance spectroscopy (NMR). These models play a central role in the investigation of the molecular basis of protein structure and function. Based on these models it is possible to identify the secondary structure elements (secondary structure) and the spatial arrangement of the polypeptide chain (fold or tertiary structure). They also reveal which atoms or amino-acid residues are buried and which are at the protein surface. The local spatial arrangement of atoms and residues can be analysed in these models, and their chemical environments characterised. Many of these models are especially informative regarding the molecular function of the respective proteins. A typical example is when they include several interacting polypeptide chains, or when they include small molecules bound at the protein surface which act as natural ligand, substrates or as inhibitors. In particular, the determinants for interaction affinity and specificity can be investigated and molecular mechanisms of binding and catalysis can be inferred using these models. Structural models can also be predicted using computational approaches as described in the Protein Structure Prediction chapter. In general predicted models are less reliable than experimental models, but there has been considerable improvement in the quality of predicted models over the last years.