Three-Dimensional Structure of Biomolecules

Every third bond in the polymer backbone chain of a protein is an amide bond. It is the fundamental building block in a protein and the mutual spatial arrangement of the sequential planar amide bonds determines its overall architecture. Typical arrangements involving the amide NH and C═O groups in hydrogen bonds result in α-helical and β-pleated sheet structures. The inversion of the polymer chain in space is achieved in turns, which can assume a variety of different geometries. Helices, sheets, and turns are the secondary structure elements. They assemble into motifs and domains to form the tertiary and quaternary structure of proteins. The function of a protein is not necessarily coupled to a particular folding pattern, however, the catalytic and ligand-functional sites within a folding class are found at the same position. Nature separates fold-stabilizing residues from functional amino acids to keep the dual optimization problem separate. Proteases specifically recognize peptide sequences by binding to well-tailored pockets on either side of the cleavage site. Peptide libraries with a photometric or fluorescent label attached can be cleaved by a protease and help to elucidate its substrate profile. Structural arrangements of molecular parts found in multiple crystal structures can be sequentially arranged in a kinematic order to give an idea of a dynamic process. The spatial arrangement of amino-acid residues that catalyze a particular chemical transformation is highly conserved and can be found in protein architectures with similar geometry even so the proteins are constructed from divergent folds. The DNA molecule encodes the genetic information and forms a double helix of two opposing strands wrapped like a handrail by sugar-phosphate polymer chains. They carry the complementary base pairs on the stacked steps of the double helix. The individual base pairs form a typical H-bonding pattern in the center of the helix. The typical H-bonding pattern of the bases allows each individual strand of DNA to be complementary to the second strand. A small and a large groove are formed between the sugar-phosphate backbone. In the large groove, the coding of the base pairs on each step can be read from the side. By complexing bases on adjacent steps with metal ions or by intercalating planar agents between these steps, the DNA is geometrically distorted and the reading of the genetic information during cell growth is inhibited. https://sn.pub/8oi55k