Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study.
The solvent structure and dynamics around ccbeta-p, a 17-residue peptide that forms a parallel three-stranded alpha-helical coiled coil in solution, was analysed through 10 ns explicit solvent molecular dynamics (MD) simulations at 278 and 330 K. Comparison with two corresponding simulations of the monomeric form of ccbeta-p was used to investigate the changes of hydration upon coiled-coil formation. Pronounced peaks in the solvent density distribution between residues Arg8 and Glu13 of neighbouring helices show the presence of water bridges between the helices of the ccbeta-p trimer; this is in agreement with the water sites observed in X-ray crystallography experiments. Interestingly, this water site is structurally conserved in many three-stranded coiled coils and, together with the Arg and Glu residues, forms part of a motif that determines three-stranded coiled-coil formation. Our findings show that little direct correlation exists between the solvent density distribution and the temporal ordering of water around the trimeric coiled coil. The MD-calculated effective residence times of up to 40 ps show rapid exchange of surface water molecules with the bulk phase, and indicate that the solvent distribution around biomolecules requires interpretation in terms of continuous density distributions rather than in terms of discrete molecules of water. Together, our study contributes to understanding the principles of three-stranded coiled-coil formation.
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, 8093 Zürich, Switzerland.
Jozica
J
Dolenc
Riccardo
R
Baron
John H
JH
Missimer
Michel O
MO
Steinmetz
Wilfred F
WF
van Gunsteren
D020816:Amino Acid Motifs; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011336:Probability; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D013696:Temperature; D013997:Time Factors; D014867:Water / Q000737:chemistry*
D010455:Peptides; D012997:Solvents; D014867:Water