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Molecular‐Dynamics Simulations of C‐ and N‐Terminal Peptide Derivatives of GCN4‐p1 in Aqueous Solution
Author(s) -
Missimer John H.,
Steinmetz Michel O.,
Jahnke Wolfgang,
Winkler Fritz K.,
van Gunsteren Wilfred F.,
Daura Xavier
Publication year - 2005
Publication title -
chemistry and biodiversity
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.427
H-Index - 70
eISSN - 1612-1880
pISSN - 1612-1872
DOI - 10.1002/cbdv.200590078
Subject(s) - chemistry , dimer , leucine zipper , salt bridge , molecular dynamics , coiled coil , helix (gastropod) , crystallography , circular dichroism , aqueous solution , monomer , peptide , amino terminal , residue (chemistry) , tetrapeptide , stereochemistry , mutant , peptide sequence , biochemistry , computational chemistry , gene , polymer , ecology , organic chemistry , biology , snail
We report the investigation of two 16‐residue peptides in aqueous solution by means of molecular‐dynamics simulations. The peptides constitute the C‐ and N‐terminal halves of the 33‐residue monomer whose dimer constitutes the leucine zipper of the yeast transcriptional activator, denoted GCN4‐p1. To examine a hypothesis about coiled‐coil formation, in which the C‐terminal half contains a helix‐formation trigger site absent in the N‐terminal half, experimental studies of the two peptides have determined their helix propensities under several conditions of temperature, pH, and salt concentration with circular dichroism. An NMR experiment provides additional evidence. At temperatures of 278 and 325 K and pH 7.5, mixtures of α ‐ and π ‐helical secondary structure constitute the most probable conformations in both C‐ and N‐terminal halves. A bifurcated salt bridge between Arg25 and Glu22/20 correlates with the structural fluctuations of the C‐terminal half. It also exhibits a persistent loop at the N‐terminal end involving the side chains of His18 and Glu22, which is reminiscent of helix‐capping boxes. Nonreversible unfolding appears to occur abruptly in the Arg25 mutant, suggesting a cooperative event. Analysis does not indicate that the N‐terminal half is less stable than the C‐terminal half, indicating that 100 ns is too short a period to observe complete unfolding.