Protein molecules, 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). 

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

It appears that the discreteness of a structure is a general principle of protein architecture, which not only reflects the evolution of the protein molecule but also has a deep physical ground (Privalov, 1985, 1986). It is just this unique thermodynamic property of the protein molecule that has made possible a quantitative definition of protein stability. 

The presence of two closely similar folding domains and the overall similarity to the riboflavin synthase fold has been confirmed recently by X-ray structure analysis. Despite that two-domain architecture, the fluorescent proteins bind only one ligand molecule per protein molecule, whereas riboflavin synthases have two ligand-binding sites per protomer. A recent mutagenesis study has located the single binding site to the N-terminal domain. ... 

The structures, the interactions, and the dynamics of proteins are fundamental to their function. The dynamic properties of proteins in the nucleus are essential for their function in nuclear architecture and gene expression. High mobility of proteins ensures their availability throughout the nucleus and the dynamic interaction creates the architectural framework for nuclear processes. Thus, nuclear morphology is shaped by the functional interactions of nuclear protein components. Studies with fluorescently tagged protein molecules reveal high mobility, compartmentation, and repeated transient interactions. 

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. 

However, in a globular protein molecule, the polypeptide adopts a specific, more or less fixed, structure. Such a compact inflexible architecture is stable only if interactions within the protein molecule and between the protein and its environment compensate for the loss of conformational entropy. 

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