Michael C. Owen

Aromatic‐backbone interactions in model α‐helical peptides

The effects on helical stability of weak polar interactions between aromatic side‐chains and the peptide backbone were examined. α‐Helical model peptides, hexa‐Ala, with sequential Tyr replacement, were investigated computationally to obtain the geometries and energetics of the interactions. Geometries were obtained with the B3LYP/6‐31G* level of theory. Interaction energies were calculated using BHandHLYP/cc‐pVTZ and an improved method to correct for basis set superposition error when fragmentation caused steric clashes. Both i, i + 1 and i, i − 4 interactions were observed when Tyr was in position i = 5. The position of the aromatic residue in the amino acid sequence was crucial in facilitating aromatic‐backbone interactions. The distance between the center of the aromatic ring of Tyr and the individual interacting backbone atoms ranged from 3.65 to 5.50 Å. The interactions have energies of the same order as hydrogen bonds and, thus, could have a significant impact on the stability of the helix.

Conformation-Dependent •OH/H2O2 Hydrogen Abstraction Reaction Cycles of Gly and Ala Residues: A Comparative Theoretical Study

To determine if (•)OH can initiate the unfolding of an amino acid residue, the elementary reaction coordinates of H abstraction by (•)OH different conformations (β(L), γ(L), γ(D), α(L), and α(D)) of Gly and Ala dimethyl amides were computed using first-principles quantum computations. The MPWKCIS1K/6-311++G(3df,2p)//BHandHLYP/6-311+G(d,p) level of theory was selected after different combinations of functionals and basis sets were compared. The structures of Gly and Ala in the elementary reaction steps were compared to the conformers of the Gly, Gly(•), Ala, and Ala(•) structures in the absence of (•)OH/H(2)O, which were identified by optimizing the minima of the respective potential energy surfaces. A dramatic change in conformation is observed in the Gly and Ala conformers after conversion to Gly(•) and Ala(•), respectively, and this change can be monitored along the minimal energy pathway. The β(L) conformer of Gly (-0.3 kJ mol(-1)) and Ala (-1.6 kJ mol(-1)) form the lowest-lying transition states in the reaction with (•)OH, whereas the side chain of Ala strongly destabilizes the α conformers compared to the γ conformers, which could cause the lower reactivity shown in Ala. This effect shown in Ala could affect the abstraction of hydrogen from Ala and the other chiral amino acid residues in the helices. The energy of subsequent hydrogen abstraction reactions between Ala(•) and Gly(•) and H(2)O(2) remains approximately 90 kJ mol(-1) below the entrance level of the (•)OH reaction, indicating that the (•)OH radical can initiate an α to β transition in an amino acid residue if a molecule such as H(2)O(2) can provide the hydrogen atom necessary to re-form Gly and Ala. This work delineates the mechanism of the rapid (•)OH-initiated unfolding of peptides and proteins which has been proposed in Alzheimers and other peptide misfolding diseases involving amyloidogenic peptides.

Development of glycyl radical parameters for the OPLS?AA/L force field

On the basis of quantum chemical calculations Cα‐glycyl radical parameters have been developed for the OPLS‐AA/L force field. The molecular mechanics hypersurface was fitted to the calculated quantum chemical surface by minimizing their molecular mechanics parameter dependent sum‐of‐squares deviations. To do this, a computer program in which the molecular mechanics energy derivatives with respect to the parameters were calculated analytically was developed, implementing the general method of Lifson and Warshel (J Chem Phys 1968, 49, 5116) for force field parameter optimization. This program, in principle, can determine the optimal parameter set in one calculation if enough representative value points on the quantum chemical potential energy surface are available and there is no linear dependency between the parameters. Some of the parameters in quantum calculations, including several new torsion types around a bond as well as angle parameters at a new central atom type, are not completely separable. Consequently, some restrictions and/or presumptions were necessary during parameter optimization. The relative OPLS‐AA energies reproduced those calculated quantum chemically almost perfectly.

Protein Stability and Unfolding Following Glycine Radical Formation

Glycine (Gly) residues are particularly susceptible to hydrogen abstraction; which results in the formation of the capto-dative stabilized Cα-centered Gly radical (GLR) on the protein backbone. We examined the effect of GLR formation on the structure of the Trp cage; tryptophan zipper; and the villin headpiece; three fast-folding and stable miniproteins; using all-atom (OPLS-AA) molecular dynamics simulations. Radicalization changes the conformation of the GLR residue and affects both neighboring residues but did not affect the stability of the Trp zipper. The stability of helices away from the radical center in villin were also affected by radicalization; and GLR in place of Gly15 caused the Trp cage to unfold within 1 µs. These results provide new evidence on the destabilizing effects of protein oxidation by reactive oxygen species.

Molecular ageing: Free radical initiated epimerization of thymopentin – A case study

The epimerization of amino acid residues increases with age in living organisms. In the present study, the structural consequences and thermodynamic functions of the epimerization of thymopentin (TP-5), the active site of the thymic hormone thymopoietin, were studied using molecular dynamics and density functional theory methods. The results show that free radical-initiated D-amino acid formation is energetically favoured (-130 kJmol(-1)) for each residue and induces significant changes to the peptide structure. In comparison to the wild-type (each residue in the L-configuration), the radius of gyration of the D-Asp(3) epimer of the peptide decreased by 0.5 Å, and disrupted the intramolecular hydrogen bonding of the native peptide. Beyond establishing important structural, energetic and thermodynamic benchmarks and reference data for the structure of TP-5, these results disseminate the understanding of molecular ageing, the epimerization of amino acid residues.