Polymerase structure-function analysis

Campbell EA, Pavlova O, Zenkin N et al (2005) Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase. EMBO J 24 674—682... 

EofF, R.L., Stafford, J.B., Szekely, J., Rizzo, C.J., Egli, M., Guengerich, F.P., and Mamett, L.J. (2009) Structural and functional analysis of Sulfolobus solfataricus Y-family DNA polymerase Dpo4-catalyzed bypass of the malondi-aldehyde-deoxyguanosine adduct. Biochemistry, 48, 7079-7088. 

In the rest of this chapter we reflect on what we have observed in our models of Pol IV and UmuC(V), and compare this to the X-ray structures for other Y-family DNA polymerases. Our laboratory has focused on the relationship between DNA polymerase structure and function for B[a]P-N2-dG adducts, which will be described below, although much of this analysis is unpublished [116]. 

Kuznedelov, K., Korzheva, N., Mustaev, A., and Severinov, K. (2002). Structure-based analysis of RNA polymerase function the largest subunits rudder contributes critically to elongation complex stability and is not involved in the maintenance of RNA-DNA hybrid length. EMBO J. 21(6), 1369-1378. 

Progress in molecular biology has provided a new perspective. Techniques such as the polymerase chain reaction and single-strand conformation polymorphism analysis have greatly facilitated the molecular analysis of erythroenzymopathies. These studies have clarified the correlation between the functional and structural abnormalities of the variant enzymes. In general, the mutations that induce an alteration of substrate binding site and/or enzyme instability might result in markedly altered enzyme properties and severe clinical symptoms. 

Fig. 6. DNA sequence analysis, (a) Simplified methodology for dideoxy sequencing. A primer, 5 -TCTA, hybridized to the template, is used to initiate synthesis by DNA polymerase, (b) Structure of 2,3,-dideoxy CTP. When no 3 -OH functionality is available to support addition of another nucleotide to the growing chain, synthesis terminates once this residue is incorporated into the synthetic reaction, (c) Representation of a DNA sequencing gel and the sequence, read from bottom to the top of the gel, gives sequence information in the conventional 5 to 3 direction.

Over the past 30 years, most of the important discoveries in the biological sciences have been associated with proteins and nucleic acids, and thus chemists have been most active in conducting their research to address the relationship between the structure and function of these macromolecules as well as to develop small molecules as mechanistic probes or drug candidates to target these two types of biopolymers. This rapid progress of development is undoubtedly due to—other than the importance of proteins and nucleic acids in biological functions—the availability of various powerful tools (such as the polymerase chain reaction, solid-phase synthesizers, sequence analysis, and sensitive assay systems) to both chemists and biologists, and the close interplay between these two disciplines. 

Carrodeguas, J. A., Theis, K., Bogenhagen, D. F., and Kisker, C. (2001). Crystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase gamma, Pol gamma B, functions as a homodimer. Mol. Cell 7, 43-54. 

Many natural biomolecules, like peptides and proteins, interact and self-assemble to form delicate structures that are associated with specific functions (33). Ligaments and hair, for example, are assembled from collagen and keratin, respectively. DNA transcription is initiated by self-assembly of transcription factors, RNA polymerase, and DNA. Systematic studies and analysis of these natural existing self-assembly systems provide insight into the chemical and structural principles of peptide self-assembly, which inspires the development of molecular self-assembly as a new approach for fabrication of novel supramolecular architectures. 

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