Nucleic acids Macromolecules with structure

Figure 1.2 General structure of a cell showing the main compartments (organelles) into which the interior is partitioned. ALL ceLLs of aLL organisms are constructed from the main bioLogicaL macromoLecuLes proteins, carbohydrates, and nucleic acids together with macromolecular lipid structures that comprise the membranes, (illustration from Philip Harris Ltd, Weston Super Mare, UK).

The Protein Data Bank (PDB) [5] is a computerized archive for the three-dimensional structural data on biological macromolecules - proteins and nucleic acids. Each protein structure reported has an identifying code (IDCODE), a header record containing useful information on the protein such as the name and source of the protein and the resolution of the structure, together with a series of references to published articles on the protein. Data are included on the refinement methods used, such as the programs used, the R value, the number of Bragg reflections, the root-mean-square deviations of the bond lengths and... 

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.)... 

The overall scope of this book is the implementation and application of available theoretical and computational methods toward understanding the structure, dynamics, and function of biological molecules, namely proteins, nucleic acids, carbohydrates, and membranes. The large number of computational tools already available in computational chemistry preclude covering all topics, as Schleyer et al. are doing in The Encyclopedia of Computational Chemistry [23]. Instead, we have attempted to create a book that covers currently available theoretical methods applicable to biomolecular research along with the appropriate computational applications. We have designed it to focus on the area of biomolecular computations with emphasis on the special requirements associated with the treatment of macromolecules. 

The mechanism of carcinogenesis by PAHs is believed to involve alkylation of an informational macromolecule in a critical, but at present unknown, manner. Such an interaction with a protein has been modelled by alkylation of a peptide this showed a conformational change occurred on alkylation. It has not yet been possible to study the structure of DNA alkylated by an activated carcinogen this is because DNA is a fiber and the structural order in it is not sufficient for a crystal structure determination. However the crystal structures of some alkylated portions of nucleic acids are described, particularly some nucleosides alkylated by chloromethyl derivatives of DMBA. In crystals of these alkylation products the PAH portion of the adduct shows a tendency to lie between the bases of other nucleoside... 

The biological applications of NMR include the study of the structure of macromolecules such as proteins and nucleic acids and the study of membranes, and enzymic reactions. Newer methods and instruments have overcome, to a large extent, the technical difficulties encountered with aqueous samples and the analysis of body fluids is possible, permitting the determination of both the content and concentration of many metabolites in urine and plasma. NMR is not a very sensitive technique and it is often necessary to concentrate the sample either by freeze drying and dissolving in a smaller volume cm- by solid phase extraction methods. 

Fluorescence spectroscopy and its applications to the physical and life sciences have evolved rapidly during the past decade. The increased interest in fluorescence appears to be due to advances in time resolution, methods of data analysis and improved instrumentation. With these advances, it is now practical to perform time-resolved measurements with enough resolution to compare the results with the structural and dynamic features of macromolecules, to probe the structures of proteins, membranes, and nucleic acids, and to acquire two-dimensional microscopic images of chemical or protein distributions in cell cultures. Advances in laser and detector technology have also resulted in renewed interest in fluorescence for clinical and analytical chemistry. 

The concept of the similarity of molecules has important ramifications for physical, chemical, and biological systems. Grunwald (7) has recently pointed out the constraints of molecular similarity on linear free energy relations and observed that Their accuracy depends upon the quality of the molecular similarity. The use of quantitative structure-activity relationships (2-6) is based on the assumption that similar molecules have similar properties. Herein we present a general and rigorous definition of molecular structural similarity. Previous research in this field has usually been concerned with sequence comparisons of macromolecules, primarily proteins and nucleic acids (7-9). In addition, there have appeared a number of ad hoc definitions of molecular similarity (10-15), many of which are subsumed in the present work. Difficulties associated with attempting to obtain precise numerical indices for qualitative molecular structural concepts have already been extensively discussed in the literature and will not be reviewed here. 

Macromolecules of biological origin perform various functions in the body. For example, proteins which perform the role of biological catalysts in the body are called enzymes, those which are crucial to communication system in the body are called receptors. Carrier proteins carry polar molecules across the cell membrane. Nucleic acids have coded genetic information for the cell. Lipids and carbohydrates are structural parts of the cell membrane. We shall explain the drug-target interaction with the examples of enzymes and receptors. 

---