Are solvation free energies of homogeneous helical peptides additive?
We investigated the additivity of the solvation free energy of amino acids in homogeneous helices of different length in water and in chloroform. Solvation free energies were computed by multiconfiguration thermodynamic integration involving extended molecular dynamics simulations and by applying the generalized-born surface area solvation model to static helix geometries. The investigation focused on homogeneous peptides composed of uncharged amino acids, where the backbone atoms are kept fixed in an ideal helical conformation. We found nonlinearity especially for short peptides, which does not allow a simple treatment of the interaction of amino acids with their surroundings. For homogeneous peptides longer than five residues, the results from both methods are in quite good agreement and solvation energies are to a good extent additive.
Staritzbichler
René
R
Center for Bioinformatics, Saarland University, Saarbrücken, Germany.
Gu
Wei
W
Helms
Volkhard
V
D000596:Amino Acids / Q000737:chemistry; D002725:Chloroform / Q000737:chemistry; D003198:Computer Simulation; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012995:Solubility; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D000596:Amino Acids; D010455:Peptides; D014867:Water; D002725:Chloroform