Architecture of Protein Molecules

The architecture of protein molecules is complex and can be described according to structural organization as primary structure (amino acid sequence), secondary structure (regular structures such as helical, pleated sheet, and coil stractures), tertiary structure (fold in three-dimensional space), quaternary structure (subunit structure) and quintemary structure (biomacromolecular complexes). Usually the overall three-dimensional (3D) architecture of a protein molecule is termed as its conformation, which refers to its secondary and tertiary structures. Between these two stractures, motifs (supersecondary structures) refer to the packing of adjacent secondary stractures into distinct structural elements and domains refer to identifiable 3D structural units that may correspond to functional units. The structures of most proteins with more than 200 amino acid residues appear to consist of two or more domains. 

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The architecture of protein molecules is quite complex. Nevertheless, this complexity can be resolved by defining various levels of structural organization. 

The structures of more than 10,000 proteins had been elucidated by NMR and x-ray crystallography by mid-2000, and several new structures are now determined each day. The coordinates are collected at the Protein Data Bank (http //www. rcsb.org/pdb) and the structures can be accessed for visualization and analysis. Knowledge of the detailed molecular architecture of proteins has been a source of insight into how proteins recognize and bind other molecules, how they function as enzymes, how they fold, and how they evolved. This extraordinarily rich harvest is continuing at a rapid pace and is greatly influencing the entire field of biochemistry. 

The complex molecular architecture of proteins and enzymes leads to more subtle aggregation properties than those of synthetic copolymers. In particular, the chirality of these biological molecules offers an extra degree of freedom to the self-assembly process. This is discussed in more detail in the next section for now we neglect the effect of chirality. 

Information regarding the shape of protein molecules may be obtained from measurements of viscosity, light scattering or streaming birefringence, aided by electron microscopy and X-ray diffraction analysis. This last technique is specially valuable since it can be used to provide not merely the overall shape of a protein molecule but also a detailed picture of its molecular architecture. 

The structure of any molecule is a unique and specific aspect of its identity. Molecular structure reaches its pinnacle in the intricate complexity of biological macromolecules, particularly the proteins. Although proteins are linear sequences of covalently linked amino acids, the course of the protein chain can turn, fold, and coil in the three dimensions of space to establish a specific, highly ordered architecture that is an identifying characteristic of the given protein molecule (Figure 1.11). 

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