1. Elements of metabolic evolution
Claudia Huber, Florian Kraus, Marianne Hanzlik, Wolfgang Eisenreich, Günter Wächtershäuser Chemistry. 2012 Feb 13;18(7):2063-80. doi: 10.1002/chem.201102914. Epub 2012 Jan 13.
Research into the origin of evolution is polarized between a genetics-first approach, with its focus on polymer replication, and a metabolism-first approach that takes aim at chemical reaction cycles. Taking the latter approach, we explored reductive carbon fixation in a volcanic hydrothermal setting, driven by the chemical potential of quenched volcanic fluids for converting volcanic C1 compounds into organic products by transition-metal catalysts. These catalysts are assumed to evolve by accepting ever-new organic products as ligands for enhancing their catalytic power, which in turn enhances the rates of synthetic pathways that give rise to ever-new organic products, with the overall effect of a self-expanding metabolism. We established HCN, CO, and CH(3)SH as carbon nutrients, CO and H(2) as reductants, and iron-group transition metals as catalysts. In one case, we employed the "cyano-system" [Ni(OH)(CN)] with [Ni(CN)(4)](2-) as the dominant nickel-cyano species. This reaction mainly produced α-amino acids and α-hydroxy acids as well as various intermediates and derivatives. An organo-metal-catalyzed mechanism is suggested that mainly builds carbon skeletons by repeated cyano insertions, with minor CO insertions in the presence of CO. The formation of elemental nickel (Ni(0)) points to an active reduced-nickel species. In another case, we employed the mercapto-carbonyl system [Co(2)(CO)(8)]/Ca(OH)(2)/CO for the double-carbonylation of mercaptans. In a "hybrid system", we combined benzyl mercaptan with the cyano system, in which [Ni(OH)(CN)] was the most productive for the double-carbon-fixation reaction. Finally, we demonstrated that the addition of products of the cyano system (Gly, Ala) to the hybrid system increased productivity. These results demonstrate the chemical possibility of metabolic evolution through rate-promotion of one synthetic reaction by the products of another.
2. Conformation-dependent ˙OH/H2O2 hydrogen abstraction reaction cycles of Gly and Ala residues: a comparative theoretical study
Michael C Owen, Milán Szori, Imre G Csizmadia, Bela Viskolcz J Phys Chem B. 2012 Jan 26;116(3):1143-54. doi: 10.1021/jp2089559. Epub 2012 Jan 10.
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 Alzheimer's and other peptide misfolding diseases involving amyloidogenic peptides.
3. Sequence isomerism-dependent self-assembly of glycopeptide mimetics with switchable antibiofilm properties
Limin Chen, Jie Feng, Dan Yang, Falin Tian, Xiaomin Ye, Qiuping Qian, Shuai Wei, Yunlong Zhou Chem Sci. 2019 Jul 11;10(35):8171-8178. doi: 10.1039/c9sc00193j. eCollection 2019 Sep 21.
In biological systems, diverse amino acid sequences and functional decorations endow proteins with specific functions. Functionally modified oligopeptides are attractive building blocks to assemble stimuli-responsive biomimetic superstructures for mimicking soft structures in nature and biomaterial applications. In this work, we selectively synthesized the structurally simplest isomeric tripeptides (i.e., Ala-Gly-Gly-OH, Gly-Ala-Gly-OH and Gly-Gly-Ala-OH) to demonstrate how the subtlest change in sequence isomerism influences the self-assembly of glycopeptides. To impart self-assembly capability and stimuli-responsiveness, the isomeric tripeptides were modified with a hydrophobic n-butylazobenzene tail at the N-terminal. We observed three different self-assembled 1-D morphologies (i.e., nanotwists, nanoribbons and nanofibers) from the azobenzene-glycopeptides (AGPs) under the same conditions when the position of the Ala residue was switched. Experimental methods including transmission electron microscopy (TEM), atomic force microscopy (AFM), X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy and circular dichroism (CD) spectroscopy were used to characterize the structural details of glycopeptide mimetic assemblies. Martini coarse-grained molecular dynamics (MD) simulations confirmed such structural observations and investigated the differences in assembly mechanisms. Furthermore, the glycopeptide mimetic assemblies showed a reversible disassembly-assembly process in response to temperature, light or host-guest chemistry, and can be used as switchable antibiofilm nanoagents.