Nucleic electron density maps

This chapter will address software systems to interactively fit molecular models to electron density maps and to analyse the resulting models. This chapter is heavily biased toward proteins, but the programs can also build nucleic acid models. First a brief review of molecular modelling and graphics is presented. Next, the best current and freely available programs are discussed with respect to their performance on common tasks. Finally, some views on the future of such software are given. 

At 6 A resolution, the macromolecule usually appears as a blob of electron density and the chain backbone is generally unrecognizable. At 3.0 A resolution, it is possible to trace the path of the macromolecular chain backbone. The double helices of nucleic acids are traced readily. At 2.0 A resolution, almost all protein side chains, nucleic acid nucleotides and polysaccharide glycoses are visible. A model of the protein, nucleic acid or glycan can be constructed if the amino acid, nucleotide or monosaccharide sequence is known. At higher resolution, individual atoms begin to be seen. It is possible to identify amino acid side chains, nucleotides and glycose units directly from the electron density map. 

At this stage we wanted to adjust the coordinates to fit both the geometry of the standard nucleotides and the electron density map. This was achieved by the use of a program REFINE 2 written by Hermans and McQueen [16, 17], as modified by Sussman [unpublished results] for nucleic acid structures. The objective of this program is to fit a flexible polymer made up of a series of residues (amino acids or... 

A more practical representation of the electron distribution in a molecule can be obtained from the probability density contour maps. Isodensity contours in the molecular plane and in a plane parallel to the molecular plane at an altitude of 0.8 atomic unit have been calculated230 for three nucleic acid bases (adenine, thymine, and cytosine) from non-empirical wave functions. The first type of contour gives an overall picture of cr-bonding in the molecule, and the second characterizes the 77-electron density. 

The method for calculating the electrostatic potential map is outlined in Reference 54, and an example of the electrostatic potential around a nucleic-acid base pair is shown in Figure 17.14. The electron density at the distance r from an atomic nucleus may be represented, as in Chapter 9, Equation 9.4, by... 

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