On the Quest of Dioxygen by Monomeric Sarcosine Oxidase. A Molecular Dynamics Investigation.
It is reported here on random acceleration molecular dynamics (RAMD) simulations with the 2GF3 bacterial monomeric sarcosine oxidase (MSOX), O2 , and furoic acid in place of sarcosine, solvated by TIP3 H2 O in a periodic box. An external tiny force, acting randomly on O2 , accelerated its relocation, from the center of activation between residue K265 and the si face of the flavin ring of the flavin adenine dinucleotide cofactor, to the surrounding solvent. Only three of the four O2 gates previously described for this system along a composite method technique were identified, while two more major O2 gates were found. The RAMD simulations also revealed that the same gate can be reached by O2 along different pathways, often involving traps for O2 . Both the residence time of O2 in the traps, and the total trajectory time for O2 getting to the solvent, could be evaluated. The new quick pathways discovered here suggest that O2 exploits all nearby interstices created by the thermal fluctuations of the protein, not having necessarily to look for the permanent large channel used for uptake of the FADH cofactor. To this regard, MSOX resembles closely KijD3 N-oxygenase. These observations solicit experimental substantiation, in a long term aim at discovering whether gates and pathways for the small gaseous ligands inside the proteins are under Darwinian functional evolution or merely stochastic control operates.
Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze, Palazzo Ducale, IT-55100 Lucca, (phone/fax: +39-0583-417336). francesco.pietra@accademialucchese.it.
Francesco
F
Pietra
D048009:Clostridium symbiosum / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D010100:Oxygen / Q000378:metabolism*; D011487:Protein Conformation; D012521:Sarcosine / Q000378:metabolism; D050879:Sarcosine Oxidase / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism*
D050879:Sarcosine Oxidase; D010100:Oxygen; D012521:Sarcosine
Monomeric sarcosine oxidase; Protein gas permeation; Random-acceleration molecular dynamics