Interactions of Phe30 in Rubredoxin Described by Ab Initio Methods. Comparison with Empirical Forcefields


L. Bendová, V. Klusák, P. Jurečka, P. Hobza, J. Vondrášek


Institute of Organic Chemistry and Biochemistry, Centre for Complex Molecular Systems and Biomolecules, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic

The protein structure is to a large extent determined by the interactions of its residues. The aromatic residues are able of hybrid interactions with several partners at once. Hence there is a strong need for studying the interactions of these residues. However, the assessment of the strength of their interactions is very complicated and not that straightforward as for classical H-bond. We decided to study the interactions on the best theoretical level available on one model system. This gives us a good reference for other, “cheaper” methods and provides us with some ideas about the roles an aromatic residue can play in the protein interior.

            Our primary criterion for the model system selection was a high X-ray structure quality and a presence of a densely packed cluster of aromatic residues with a phenylalanine having at least five residues closer than 4Å. We have chosen a small (52 AAs) thermostable FeS protein rubredoxin (desulfovibrio vulgaris) which is assumed to serve as an electron transfer protein. The hydrophobic core of the protein is constituted of several aromatic and aliphatic residues. For the purpose of our study we have chosen Phe30 which has in its vicinity an extraordinary number of interacting partners of different character. The residue is acting at once in CH/π, π/π, kation/π, anion/π (the sidechain) interactions as well as in a classical H-bond (the mainchain). The interaction energies of the central Phe30 with its partners represented as isolated amino acid molecules were calculated in vacuo using high-level ab initio methods. The positions of all non-hydrogen atoms were held fix at the X-ray structure geometry, while the position of all hydrogen atoms was optimized at the DFT/6-31G** level. The interaction energy was then calculated as the sum of two contributions; one being an RI-MP2 interaction energy extrapolated to the basis set limit, the other a correction term for higher order (CCSD(T)) correlation energy. As a test of the reliability of various empirical potentials we have computed the interaction energies of the same systems in several common forcefields.

Our present results show that there is a strong interaction of Phe30 with the surrounding residues without any repulsion.  Such strength could be the reason for thermostability of the protein and also an origin of the folding process. There is pronounced difference in the performance of the tested forcefields. Some forcefields proved to be able to reproduce the results of the reference method.