Water-mediated contacts in the trp-repressor operator complex recognition process

摘要: Water-mediated contacts are known as an important recognition tool in trp-repressor operator systems. One of these involves two conserved base pairs (G(6).C(-6) and A(5). T(-5)) three amino acids (Lys 72, Ile 79, Ala 80). To investigate the nature contacts, we analyzed X-ray structure (PDB code: 1TRO) complex by means molecular dynamics simulations. This contains dimers that exhibit structural differences. From different starting structures, 10 ns simulations have been performed. Both our show increase water molecules major groove at one side dimer, while other remains unchanged compared to structure. Though maximum residence time concerned decreases with solvent interface, continue play role mediating DNA-protein contacts. is shown new stable acids-DNA distances a long free DNA simulation. maintain stability preferential binding site on O6(G6) extended. extension agrees mutation experiment data A5 G6, which shows relative affinity due bases [A. Joachimiak, T. E. Haran, P. B. Sigler, EMBO Journal 1994, Vol. 13, No. (2) pp. 367-372]. Due rearrangements system, phosphate G6 able interconvert B(II) substate, not observed half complex. The decrease number hydrogen bonds between protein backbone could be initial step dissociation process complex, or words intermediate conformation association process. Thus, surmise features importance water-mediated