Nucleic acids crystallization problems with

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

If the intensity and phase of each individual reflection could be determined, the electron density at any position in the unit cell could be calculated, hence revealing the molecular structure. Unfortunately, the phase cannot be measured using X-rays. This is not a problem for simple crystals with only a few atoms, since there are only a very limited number of ways that the phase can be assigned. However, this is not possible for macromolecules like proteins or nucleic acids, and various approaches are used to get around this phase problem . 

Tubule obstruction. Given certain physicochemical conditions, crystals can deposit within the tubular lumen. Methotrexate, for example, is relatively insoluble at low pH and can precipitate in the distal nephron when the urine is acid. Similarly the uric acid produced by the metabolism of nucleic acids released during rapid tumour cell lysis can cause a fatal urate nephropathy. This was a particular problem with the introduction of chemotherapy for leukaemias until the introduction of allopurinol it is now routinely given before the start of chemotherapy to block xanthine oxidase so that the much more soluble uric acid precursor, hypoxanthine, is excreted instead. Crystal-nephropathy is also a... 

When we became seriously concerned about this problem (about 1985 ), it could not be convincingly decided which of these basic alternatives was correct (Hartree-Fock or X-ray), and it was not possible to proceed further. Subseqently, however, computers developed to the point where it became possible to carry out what are now considered modest quantum mechanical calculations directly on the nucleic acid base molecules. When this was done, it was found that the main problem did not lie in the molecular mechanics approximations themselves, nor did it lie in the experimental comparison of a crystal stracture with a gas-phase structure. Rather, the major problem... 

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