Functional assessment of “in vivo” and “in silico” mutations in the guanine binding site of RNase T1: A DFT study

Experimentally, the functional assessment of amino acid side chains in proteins is carried out by comparing parameters such as binding constants for the wild‐type protein and a mutant protein in which the considered side chain is deleted. In the present study, we apply a density functional theory (DFT) methodology to obtain changes in binding energy upon mutations in the enzyme ribonuclease T₁. Mutant structures were either taken directly from crystallographic data (“in vivo”) allowing for conformational changes upon mutation, or derived from the wild‐type (“in silico”). Excluding entropic contributions, the computed interaction energy changes upon mutation in vivo correlate qualitatively well with experimental binding free energy changes. In contrast, the in silico approach does not perform as well, especially for residues that contribute largely to binding. Subsequently, we assessed the applicability of the in vivo approach by analyzing the functional cooperativity between pairs of side chains. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Description of the S1(ππ*) state and the reinterpretation of the (1+1) REMPI spectra of N-methylpyrrole as based on the ab intio calculation: a computational spectroscopy

The ab intio calculation was performed to establish the assignment of the title spectra by such as searching for stationary points belonging to lower excited states. The lowest excited state was confirmed to be of ππ* type with an A″ symmetry of a molecular point group C_s (against the previous assumption of πΣ* type) trapped in deep potential minima at the nonplanar staggered conformation (also against the current belief on the involvement of internal rotation). Thus, lower ‘vibrational’ levels in the S₁ state were shown to be tunnel-split levels with various symmetry species for a molecular symmetry group G₁₂. Based on this finding, the spectral data as reported by Philis [Chem. Phys. Lett. 353 (2002) 84] were reassigned while applying the formalism as will be presented in Appendix A.