| Abstract | By means of combined MD and QM/MM calculation we show that this conformation positions the NH backbone towards the sulfenic acid and promotes the reaction to yield the sulfenyl amide intermediate, in one step with the concomitant release of a water molecule . |
| Protein structure selection, search parameters and Cys environment characterization | Each protein was then immersed in a truncated octahedral box of TIP3P water consisting in 8,776 water molecules , which corresponds to a 10 A distance between the protein surface and the box boundary [48]. |
| QM/MM methods | The first step consists of the breakage of the S-OH bond (with OH leaving as a water molecule after proton transfer from H20 or H3O+) and the formation of the SN bond using the following reaction coordinate |
| QM/MM methods | The second step involves the transfer of the amide proton to a water molecule , regenerating the H20 or H3O+molecule. |
| QM/MM methods | In the case of the peptide, the QM system comprises the whole peptide (ACE-Cys-SOH-NME), H3O+ molecule and the closest 9 water molecules to the system. |
| Results | To test this idea, we included in the QM system 10 water molecules and explicitly promoted proton transfer from the solvent to the S-OH group. |
| Results | 4 shows a completely broken SO bond, a well formed water molecule and the S and N atoms quite close at a distance of 1.93 angstroms. |
| Results | We observe only an increase in the OS atom that is due to its transfer from the sulfenic molecule to form a water molecule . |