Phe, Tyr, and Trp: Conformational Study of Ionic and Dimeric Forms

This study presents an in-depth conformational analysis of three aromatic amino acids tryptophan, phenylalanine, and tyrosine along with their ionic and zwitterionic forms, using first-principles calculations. For each amino acid, extensive potential energy surface scans revealed numerous stable conformers, including over 50 unique dimeric structures for each. Stabilization of these structures arises from a rich interplay of noncovalent interactions such as hydrogen bonds (especially NH-O), pi-pi stacking, CH-pi, NH-pi, and OH-pi interactions. Monomeric forms favored conformations with strong intramolecular hydrogen bonding, while dimeric forms demonstrated a balance between hydrogen bonding and aromatic interactions. Atoms-in-molecules analysis provided further insight into the strength and nature of these interactions. Comparative observations with Protein Data Bank structures highlighted geometry-dependent preferences: pi-pi stacking dominates at close range, while T-shaped CH-pi interactions are more prevalent at longer distances. These findings illuminate the intricate noncovalent landscape shaping amino acid conformations in biological systems.

Autorentext
Dr. Uppula Purushotham is a computational chemist with a Ph.D. from CSIR-IICT Hyderabad and postdoctoral research at Nagoya University, Japan. His work focuses on Ai applications in drug design, and materials science, with expertise in quantum chemistry and molecular modelling.