Structure representation macromolecules

Sequence analysis is a core area of bioinformatics research. There are four basic levels of biological structure (Table 1), termed primary, secondary, tertiary, and quaternary structure. Primary structure refers to the representation of a linear, hetero-polymeric macromolecule as a string of monomeric units. For example, the primary structure of DNA is represented as a string of nucleotides (G, C, A, T). Secondary structure refers to the local three-dimensional shape in subsections of macromolecules. For example, the alpha- and beta-sheets in protein structures are examples of secondary structure. Tertiary structure refers to the overall three-dimensional shape of a macromolecule, as in the crystal structure of an entire protein. Finally, quaternary structure represents macromolecule interactions, such as the way different peptide chains dimerize into a single functional protein. 

Figure 1-2 Schematic Representation of the Formation of a Hydrophobic Bond by Apolar Group in an Aqueous Environment. Open circles represent water. Source From I.M. Klotz, Role of Water Structure in Macromolecules, Federation Proceedings, Vol. 24, Suppl. 15, pp. S24-S33,1965.

D structural coordinates The protein is composed of a chain of amino acids, which in turn are composed of atoms. The position of these atoms can be inferred from experimental measurements, most prominently, X-ray diffraction patterns or NMR spectra. Therefore, a very detailed description of a protein is given by the exact (x, y, z) coordinates of all the protein s atoms. It has to be kept in mind, however, that structure coordinates are still an abstraction of the protein in its actual environment interacting with solvent and/or other macromolecules. This is due to experimental measurement errors, crystallization effects, and the static picture implicated by the coordinates. In addition, it is not necessarily true, that the most accurate or comprehensive information, say regarding protein function, can be inferred best from the most detailed structural representation. 

Macromolecules, including biopolymers, represent a challenge in generating meaningful structure representations and corresponding names, because frequently complete structural information is not known. Illustrations are shown from existing recommendations of the International Union of Pure and Applied Chemistry (lUPAC), and the International Union of Biochemistry (lUB). Examples from drafts under consideration by the lUPAC Commission on Macromolecular Nomenclature are also presented. Current handling of macromolecules by Chemical Abstracts Service (CAS) as well as some enhancements under development are illustrated. 

A variety of theories for flexible macromolecules (rod, spheres, cylinders, etc.) have been proposed, many of them being geared toward the study of polymers and DNA (see Conformational Sampling Conformational Search Linear Chains Conformational Search Proteins and Polymers Structural Representation), A brief discussion of representative methodologies for polymers, proteins, and nucleic acids follows. 

Inorganic Three-dimensional Structure Databases Molecular Docking and Structure-based Design Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Databases Structure Representation Three-dimensional Structure Searching,... 

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

An unsegregated-structured two-compartment representation considers biomass as being divided into two compartments, the K-compartment and the G-compartment. These two compartments contain specific groupings of macromolecules, namely the K-compartment is identified with RNA, carbohydrates and monomers of macromolecules, while the G-compartment is identified with proteins, DNA and lipids. 

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