title: A consistent force field parameter set for zwitterionic amino acid residues.
abstract: Isolated amino acids play an important role in biochemistry and are therefore an interesting object of study. Atomistic molecular dynamics (MD) simulations can provide a high-resolution picture of the dynamic features of these species, especially in their biological environment. Unfortunately, most standard force field packages lack libraries for isolated amino acids in their zwitterionic form. Although several studies have used ad-hoc parameterizations for single amino acids, a consistent force-field parameter set for these molecules is still missing. Here, we present such a parameter library derived from the widely used parm99SB set from the AMBER program package. The parameter derivation for all 20 proteinogenic amino acids transparently followed established procedures with histidine treated in three different protonation states. All amino acids were subjected to MD simulations in four different forms for comparison: zwitterionic, N-teminally capped with acetyl, C-terminally capped with N-methyl, and capped at both termini. Simulation results show similarities between the different forms. Five zwitterionic amino acids-arginine, glutamate, glycine, phenylalanine, leucine-were simulated in a protein environment. Proteins and ligands generally retained their initial structure. The new parameter set will thus facilitate future atomistic simulations of these species.
authors.affiliation: Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstr. 17, 91054, Erlangen, Germany, Anselm.Horn@fau.de.
authors.forename: Anselm H C
authors.initials: AH
authors.lastname: Horn
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D001120:Arginine / Q000737:chemistry; D018698:Glutamic Acid / Q000737:chemistry; D005998:Glycine / Q000737:chemistry; D007930:Leucine / Q000737:chemistry; D008024:Ligands; D056004:Molecular Dynamics Simulation; D010649:Phenylalanine / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
chemical_list: D000596:Amino Acids; D008024:Ligands; D014867:Water; D018698:Glutamic Acid; D010649:Phenylalanine; D001120:Arginine; D007930:Leucine; D005998:Glycine