The potential of mean force of interacting aromatic amino acids is calculated using molecular dynamics simulations. The free energy surface is determined in order to study stacking and T-shape competition for phenylalanine-phenylalanine (Phe-Phe), phenylalanine-tyrosine (Phe-Tyr), and tyrosine-tyrosine (Tyr-Tyr) complexes in vacuo, water, carbon tetrachloride, and methanol. Stacked structures are favored in all solvents with the exception of the Tyr-Tyr complex in carbon tetrachloride, where T-shaped structures are also important. The effect of anchoring the two alpha-carbons (C(alpha)) at selected distances is investigated. We find that short and large C(alpha)-C(alpha) distances favor stacked and T-shaped structures, respectively. We analyze a set of 2396 protein structures resolved experimentally. Comparison of theoretical free energies for the complexes to the experimental analogue shows that Tyr-Tyr interaction occurs mainly at the protein surface, while Phe-Tyr and Phe-Phe interactions are more frequent in the hydrophobic protein core. This is confirmed by the Voronoi polyhedron analysis on the database protein structures. As found from the free energy calculation, analysis of the protein database has shown that proximal and distal interacting aromatic residues are predominantly stacked and T-shaped, respectively.

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A B S T R A C TWe have applied a computational strategy, using a combination of virtual screening, docking and molecular dynamics techniques, aimed at identifying possible lead compounds for the non-covalent inhibition of the main protease 3CL pro of the SARS-CoV2 Coronavirus. Based on the X-ray structure (PDB code: 6LU7), ligands were generated using a multimodal structure-based design and then docked to the monomer in the active state. Docking calculations show that ligand-binding is strikingly similar in SARS-CoV and SARS-CoV2 main proteases. The most potent docked ligands are found to share a common binding pattern with aromatic moieties connected by rotatable bonds in a pseudo-linear arrangement.

In this paper we compare the polarization response given by two different chemical potential equalization schemes to be applied to molecular dynamics simulations: the standard fluctuating point charge model (FQ) and the atom–atom charge transfer model (AACT). We have tested the transferability of FQ and AACT parameters, fitted to the polarizability of small size alkanes and polyenes, to large size homologues. We show that the FQ scheme is not adequate for the n-alkanes as it strongly overestimates the polarizability tensor components as the number of carbon atoms increases. The FQ approach has been found more predictive for highly conjugated systems like polyenes, although still unsatisfactory. The AACT parameters tuned on ethane are instead perfectly transferable to alkanes of any length and conformation. The AACT scheme satisfactorily reproduces the polarization response also for highly conjugated systems.

We propose a new approach for the umbrella sampling method in molecular dynamics simulations of complex systems. An accelerated sampling of the slow degrees of freedom is achieved by generating a single self-adaptive trajectory that tends to span uniformly the reaction coordinate using a time dependent bias potential derived from the preceding history of the system. To show the convergent behavior and the efficiency of the method, we present the free energy surface of alanine dipeptide in water as a function of the backbone dihedral angles.