Protein Structure Analysis
This chapter discusses briefly structure prediction and focuses mostly on protein structure comparison. The protein folding process starts even before the nascent chain leaves the ribosome and usually converges into a stable conformation within a fraction of a second. The 3D structure of a protein can be determined experimentally using X-ray diffraction of protein crystals or Nuclear Magnetic Resonance (NMR) of proteins enriched with NMR active atoms. The term secondary structure refers to local structural arrangements of short segments along the protein polypeptide chain, usually between three and ten residue long, which are formed during the protein folding process. Homologous proteins typically share the same core structure, and the structural differences lie mostly in the loop regions, which tend to be closer to the surface of the protein and more exposed. Loop regions typically contain coils of different shapes.