Water‐mediated contacts in thetrp‐repressor operator complex recognition process

Abstract

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

Structures of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets

“…Some water-mediated interactions are energetically quite favorable and can be trapped in the crystal structure. This result is consistent with previous observations of solvent present on protein-DNA interfaces (18)(19)(20)(21)(22)(23)(24)(25)(26).…”

Structural and Thermodynamic Basis for Enhanced DNA Binding by a Promiscuous Mutant EcoRI Endonuclease

“…(There was no significant difference in the stripped and unstripped starting structures.) Simulations of the Trp repressor-operator complex (Wibowo et al, 2004) also showed that water molecules with multi-ns residence times participate in contacts that are critical to complex stability as deduced from site-directed mutagenesis studies (Joachimiak et al, 1994).…”

Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study

“…The BI or BII DNA backbone conformation is characterized by the difference in torsion angles ϵ and ζ [(ϵ − ζ) is negative in BI and positive in BII]. BII is a conformational sub‐state of B‐DNA which has been observed to play a key role in DNA‐protein recognition,17 and the BI ↔ BII transition has been investigated in several studies 18–25…”