Computations of 36 Tautomer/Isomer Equilibria of Different Lactams

Gas-phase energies of 36 tautomer/isomer pairs of 18 six-membered N-heterocyclic compounds were computed quantum chemically. Among the considered B3LYP, BH&HLYP, BH&HLYP­(G), and PW6B95 DFT functionals, the latter two provide accurate tautomer/isomer pair energies with root-mean-square deviations (rmsd) relative to experiments of 0.2 and 0.3 kcal/mol, respectively. Since only few (namely five) experimental data are available, 15 tautomer/isomer pair energies were computed with the very precise QCISD­(T)­(quadruple-ζ) method serving as reference. Relative to this reference the PW6B95 DFT functional is slightly superior to the BH&HLYP­(G) functional, yielding an rmsd of 0.7 and 0.8 kcal/mol, respectively. In contrast to BH&HLYP­(G), the PW6B95 DFT functional yields also accurate tautomer/isomer pair energies if zwitterionic structures are involved. The tautomer/isomer pair states possess different amounts of aromaticity. This is characterized by nucleus-independent chemical shift (NICS) values. The tautomer/isomer pair reference energies, from which the energies computed with PW6B95 are subtracted, correlate linearly with the corresponding differences in the NICS values. This correlation is used to construct a correction term for the pair energies computed with PW6B95, yielding tautomer/isomer pair energies with rmsd of 0.3 kcal/mol with respect to the more CPU time demanding QCISD­(T)­(quadruple-ζ) method

Exploring the Possible Role of Glu286 in C<i>c</i>O by Electrostatic Energy Computations Combined with Molecular Dynamics

Cytochrome <i>c</i> oxidase (C<i>c</i>O) is a central enzyme in aerobic life catalyzing the conversion of molecular oxygen to water and utilizing the chemical energy to pump protons and establish an electrochemical gradient. Despite intense research, it is not understood how C<i>c</i>O achieves unidirectional proton transport and avoids short circuiting the proton pump. Within this work, we analyzed the potential role of Glu286 as a proton valve. We performed unconstrained MD simulations of C<i>c</i>O with an explicit membrane for up to 80 ns. Those MD simulations revealed that deprotonated Glu286 (Glu286-) is repelled by the negatively charged propionic acid PRD of heme a₃. Thus, it destabilizes a potential linear chain of waters in the hydrophobic cavity connecting Glu286 with PRD and the binuclear center (BNC). Conversely, protonated Glu286 (Glu286H) may remain in an upward position (oriented toward PRD) and can stabilize the connecting linear water chain in the hydrophobic cavity. We calculated the p<i>K</i>_a of Glu286 under physiological conditions to be above 12, but this value decreases to about 9 under increased water accessibility of Glu286. The latter value is in accordance with experimental measurements. In the time course of MD simulation, we also observed conformations where Glu286 bridges between water molecules located on both sides (the D channel being connected to the N side and the hydrophobic cavity), which might lead to proton backflow

Understanding Selectin Counter-Receptor Binding from Electrostatic Energy Computations and Experimental Binding Studies

Higher organisms defend themselves against invading micro-organisms and harmful substances with their immune system. Key players of the immune system are the white blood cells (WBC), which in case of infection move in an extravasation process from blood vessels toward infected tissue promoting inflammation. This process starts with the attachment of the WBC to the blood vessel wall, mediated by protein pair interactions of selectins and counter-receptors (C-R). Individual selectin C-R binding is weak and varies only moderately between the three selectin types. Multivalency enhances such small differences, rendering selectin-binding type specific. In this work, we study selectin C-R binding, the initial step of extravasation. We performed electrostatic energy computations based on the crystal structure of one selectin type co-crystallized with the ligating part of the C-R. The agreement with measured free energies of binding is satisfactory. Additionally, we modeled selectin mutant structures in order to explain differences in binding of the different selectin types. To verify our modeling procedures, surface plasmon resonance data were measured for several mutants and compared with computed binding affinities. Binding affinities computed with soaked rather than co-crystallized selectin C-R structures do not agree with measured data. Hence, these structures are inappropriate to describe the binding mode. The analysis of selectin/C-R binding unravels the role played by individual molecular components in the binding event. This opens new avenues to prevent immune system malfunction, designing drugs that can control inflammatory processes by moderating selectin C-R binding