Mapping the hydropathy of amino acids based on their local solvation structure.
In spite of its relevant biological role, no general consensus exists on the quantitative characterization of amino acid's hydropathy. In particular, many hydrophobicity scales exist, often producing quite different rankings for the amino acids. To make progress toward a systematic classification, we analyze amino acids' hydropathy based on the orientation of water molecules at a given distance from them as computed from molecular dynamics simulations. In contrast with what is usually done, we argue that assigning a single number is not enough to characterize the properties of an amino acid, in particular when both hydrophobic and hydrophilic regions are present in a residue. Instead we show that appropriately defined conditional probability densities can be used to map the hydrophilic and hydrophobic groups on the amino acids with greater detail than possible with other available methods. Three indicators are then defined based on the features of these probabilities to quantify the specific hydrophobicity and hydrophilicity of each amino acid. The characterization that we propose can be used to understand some of the ambiguities in the ranking of amino acids in the current scales. The quantitative indicators can also be used in combination with standard bioinformatics tools to predict the location of transmembrane regions of proteins. The method is sensitive to the specific environment of the amino acids and can be applied to unnatural and modified amino acids, as well as to other small organic molecules.
Department of Physics, Sapienza University of Rome , Ple A. Moro 5, 00185 Rome, Italy.
S
S
Bonella
D
D
Raimondo
E
E
Milanetti
A
A
Tramontano
G
G
Ciccotti
D000596:Amino Acids / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D014867:Water / Q000737:chemistry
D000596:Amino Acids; D014867:Water