title: Dependence of the L-alanyl-L-alanine conformation on molecular charge determined from ab initio computations and NMR spectra.
abstract: The l-alanyl-l-alanine (AA) molecule behaves differently in acidic, neutral, and basic environments. Because of its molecular flexibility and strong interaction with the aqueous environment, its behavior has to be deduced from the NMR spectra indirectly, using statistical methods and comparison with ab initio predictions of geometric and spectral parameters. In this study, chemical shifts and indirect spin-spin coupling constants of the AA cation, anion, and zwitterion were measured and compared to values obtained by density functional computations for various conformers of the dipeptide. The accuracy and sensitivity of the quantum methods to the molecular charge was also tested on the (mono)-alanine molecule. Probable AA conformers could be identified at two-dimensional potential energy surfaces and verified by the comparison of the computed parameters with measured NMR data. The results indicate that, whereas the main-chain peptide conformations of the cationic (AA+) and zwitterionic (AAZW) forms are similar, the anion (AA-) adopts also another, approximately equally populated conformer in the aqueous solution. Additionally, the NH2 group can rotate in the two main chain conformations of the anionic form AA-. According to a vibrational quantum analysis of the two-dimensional energy surfaces, higher-energy conformers might exist for all three charged AA forms but cannot be detected directly by NMR spectroscopy because of their small populations and short lifetimes. In accord with previous studies, the NMR parameters, particularly the indirect nuclear spin-spin coupling constants, often provided an excellent probe of a local conformation. Generalization to peptides and proteins, however, has to take into account the environment, molecular charge, and flexibility of the peptide chain.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nAm. 2, 16610, Prague 6, Czech Republic.
authors.forename: Vladimír
authors.initials: V
authors.lastname: Sychrovský
authors.forename: Milos
authors.initials: M
authors.lastname: Budesínský
authors.forename: Ladislav
authors.initials: L
authors.lastname: Benda
authors.forename: Vladimír
authors.initials: V
authors.lastname: Spirko
authors.forename: Zuzana
authors.initials: Z
authors.lastname: Vokacova
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Sebestík
authors.forename: Petr
authors.initials: P
authors.lastname: Bour
mesh_terms: D004151:Dipeptides / Q000737:chemistry*; D004563:Electrochemistry; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D011487:Protein Conformation; D012997:Solvents
chemical_list: D004151:Dipeptides; D012997:Solvents; C002956:alanylalanine