Oligomer structures: overview

Recent reviews from this Laboratory provide an overview of the literature of MD simulations on DNA oligomers through 1993 (27) and theoretical and computational aspects of DNA hydration (28) and counterion atmosphere (29). References to the most recent literature can be found in (30). Experimental data for comparison with MD results are available for crystal structures in the Nucleic acids Data Bank (NDB) (31), and for NMR structure in a review by Ulyanov and James (52). The research described in this article is directed towards understanding the dynamical structure of the various right-handed helical forms of DNA, their deformations and interconversions. The canonical A and B structures of DNA are shown for reference in Figure 1. The A and B forms are distinguishable in three major ways the displacement of nucleotide base pairs from the helix axis, the inclination of base pairs with respect to the helix axis, and sugar puckers. Details on these and other structural features of DNA relevant to MD analysis is readily available (33). 

In this section, a brief overview of the structural characteristics of the food proteins most widely used in studies on protein-protein complex formation is presented. Proteins presented below and in Table 1 are from milk [p-lactoglobulin (P-Lg), a-lactalbumin (a-La), bovine serum albumin (BSA), lactoferrin, caseins] or egg white (ovalbumin, lysozyme), even if proteins from other sources (including gelatin and soy and wheat proteins) are also used for self-assemblies and complex formation studies. The proteins presented are mainly monomers, but are able to self-assemble into oligomers or aggregates in some specific conditions. These conditions are also addressed. 

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