Figure 2 - uploaded by Eduard Schreiner
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Full peptide synthesis cycle comprising input of an amino acid (or peptide), here glycine, and its activation followed by elongation using another amino acid (or peptide), here another glycine, as well as termination and hydrolysis as a major reverse reaction. The calculated free energy barriers (given in k B T energy units) for individual steps of the mechanism leading to diglycine formation are colour coded. Blue: ambient bulk water (ABW), green: hot-pressurized bulk water (HPW), red: hot-pressurized water at the pyrite interface (PIW). The crossed direct formation path C ′ is very unlikely in view of its high activation free energy compared to the indirect path via isocyanate 4. See Ref. 12 for details.
Source publication
Forschungszentrum ulich GmbH, ulich Supercomputing Centre (JSC), John von Neumann Institute for Computing (NIC), Schriften des Forschungszentrums ulich, IAS Series, Vol. 3, ISBN 978-3-89336-606-4, pp. 111-118.
Contexts in source publication
Context 1
... water at the pyrite interface (PIW). The effective free energy barriers es- timated along the peptide synthesis cycle leading to diglycine are reported in Figure 2. ...
Context 2
... is evident from the mechanism depicted in Figure 2 that it is the neutral form of the amino acid glycine 2 that is required and not the zwitterionic form 1 for its reaction with the COS molecule to form thiocarbamate (see step B). The thiocarbamate 3, in turn, leads to an activated amino acid in form of its so-called Leuchs anhydride 5 that easily adds to another amino acid (or peptide) to form a peptide bond (in step E) which finally yields an elongated peptide. ...
Context 3
... it was found that these extreme HPW conditions speed up the production of peptides by accelerating individual steps of the whole peptide synthesis cycle according to the free energy barriers reported in Figure 2. Another discovery from our simulations is the so-called isocyanate pathway leading to the formation of the activated form of amino acid, Leuchs anhydride 5, from thiocarbamate 3. Compared to a direct cyclization of the thiocarbamate 3 to form Leuchs anhydride 5, the indirect isocyanate pathway, i. e. first forming an isocyanate 4 which rapidly cyclizes to Leuchs anhydride, is very much lower in terms of free energy barriers. ...
Context 4
... a significant step forward, the cycle in Figure 2 is based on a set of disconnected free energy calculations whereas a single, global free energy landscape is necessary to fully explore this rather complex reaction network including the roles of reverse and side reac- tions. This, again, will be a challenge to both algorithms to sample free energies beyond three or four dimensions and platforms to carry out such a unified, ultramassive simula- tion. ...
