The nature of intermolecular interactions between aromatic amino acid residues

Abstract

The nature of intermolecular interactions between aromatic amino acid residues has been investigated by a combination of molecular dynamics and ab initio methods. The potential energy surface of various interacting pairs, including tryptophan, phenilalanine, and tyrosine, was scanned for determining all the relevant local minima by a combined molecular dynamics and conjugate gradient methodology with the AMBER force field. For each of these minima, single-point correlated ab initio calculations of the binding energy were performed. The agreement between empirical force field and ab initio binding energies of the minimum energy structures is excellent. Aromatic-aromatic interactions can be rationalized on the basis of electrostatic and van der Waals interactions, whereas charge transfer or polarization phenomena are small for all intermolecular complexes and, particularly, for stacked structures. Proteins 2002;48:117-125.

Interaction of the Aromatics Tyr-72/Trp-288 in the Interface of the Extracellular and Transmembrane Domains Is Essential for Proton Gating of Acid-sensing Ion Channels

“…This competition is strongly affected by polarity of the environment and the ability of the surrounding solvent to form hydrogen bonds. In the crystal structure of cASIC1, Tyr-72 and Trp-288 adopt a T-shape structure; whether this geometry changes in the open, closed, and desensitized states is not known, although the binding energy differences for Tyr/Trp pair would be in the order of 1 kcal/mol going from T-shaped to intermediate stacked and 1.6 kcal/mol to the staked geometry according to previous calculations (17). These values are in the range of energy change between the open and close conformations of ASIC1.…”

Analysis of Anisotropic Side-chain Packing in Proteins and Application to High-resolution Structure Prediction

“…6 We found that there was a reasonable correlation between the two landscapes, and that molecular mechanics landscapes in turn were correlated to some extent with the distributions of side-chain packing geometries in protein structures. This and the other studies 5,9 suggested that molecular mechanics potentials capture p-p and cation-p interactions to an extent greater than might be expected for simple point charge-based models, but that there is still considerable room for improvement.…”

“…p-p, cation-p and hydrophobic interactions play important roles in stabilizing protein structures and have been investigated using quantum chemistry calculations, [3][4][5][6][7][8][9][10][11][12][13][14] molecular mechanics calculations, 5,9,15,16 and protein structural analysis. [17][18][19][20][21][22][23] Quantum chemistry and molecular mechanics calculations have identified the energy minima for pairs of interacting residues, and protein structural analysis has described the distributions of interaction geometries for different residue pairs.…”

Improvement of a FRET-based Indicator for cAMP by Linker Design and Stabilization of Donor–Acceptor Interaction

“…On the contrary, the stacking interactions between Tyr10 and the second YPY motif in L22 C may provide an important source of stabilization. 14 We therefore removed Lys2 to avoid the formation of H-bonds and, similarly, Tyr3 and Pro4 were removed to reduce the size of the hydrophobic cluster. Additionally a glutamic acid was placed at position 2 to increase the repulsion with Asp6, 9,17 and 20.…”