Networks of water molecules in a proflavine deoxydinucleoside phosphate complex.
Using previously reported ab-initio atom-atom potentials for the interactions of a water molecule with phosphates, sugars and bases and newly computed ab-initio atom-atom potentials for the interaction between a proflavine ion and water, we have analyzed with the Monte-Carlo Metropolis method networks of water molecules hydrating a 2:2 complex of proflavine and deoxycytidylyl-3',5'-guanosine, recently studied with X-ray crystallography. From our simulations we have i) verified the quality of our atom-atom potentials by obtaining patterns of oxygen atoms in very good agreement with the X-ray patterns for the minor groove and in reasonable agreement in the major groove, ii) predicted the water's hydrogen atoms positions and iii) preliminarily predicted the number of water molecules not reported in the X-ray study but present in the major groove. The above data, even if preliminary, and the analyses on the energetics of the water-water, water-proflavine and water-dCpG interactions indicate that very detailed accounts on the water filaments in the above crystal can be obtained optimally by merging computer and X-ray experiments.
D000166:Acridines; D003198:Computer Simulation; D003845:Deoxycytosine Nucleotides; D003849:Deoxyguanosine / Q000031:analogs & derivatives*; D008968:Molecular Conformation; D015394:Molecular Structure; D009010:Monte Carlo Method; D011370:Proflavine; D013816:Thermodynamics; D014867:Water; D014961:X-Ray Diffraction
D000166:Acridines; D003845:Deoxycytosine Nucleotides; D014867:Water; C037781:deoxycytidylyl-(3'-5')-deoxyguanosine; D011370:Proflavine; D003849:Deoxyguanosine