دورية أكاديمية
On the Quest of Dioxygen by Monomeric Sarcosine Oxidase. A Molecular Dynamics Investigation.
| العنوان: | On the Quest of Dioxygen by Monomeric Sarcosine Oxidase. A Molecular Dynamics Investigation. |
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| المؤلفون: | Pietra F; Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze, Palazzo Ducale, IT-55100 Lucca, (phone/fax: +39-0583-417336). francesco.pietra@accademialucchese.it. |
| المصدر: | Chemistry & biodiversity [Chem Biodivers] 2015 Aug; Vol. 12 (8), pp. 1163-71. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Verlag Helvetica Chimica Acta Country of Publication: Switzerland NLM ID: 101197449 Publication Model: Print Cited Medium: Internet ISSN: 1612-1880 (Electronic) Linking ISSN: 16121872 NLM ISO Abbreviation: Chem Biodivers Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Zürich, Switzerland : Hoboken, NJ : Verlag Helvetica Chimica Acta ; Distributed in the USA by Wiley, c2004- |
| مواضيع طبية MeSH: | Clostridium symbiosum/*enzymology , Oxygen/*metabolism , Sarcosine Oxidase/*metabolism, Clostridium symbiosum/chemistry ; Clostridium symbiosum/metabolism ; Molecular Dynamics Simulation ; Protein Conformation ; Sarcosine/metabolism ; Sarcosine Oxidase/antagonists & inhibitors ; Sarcosine Oxidase/chemistry |
| مستخلص: | 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. (Copyright © 2015 Verlag Helvetica Chimica Acta AG, Zürich.) |
| فهرسة مساهمة: | Keywords: Monomeric sarcosine oxidase; Protein gas permeation; Random-acceleration molecular dynamics |
| المشرفين على المادة: | EC 1.5.3.1 (Sarcosine Oxidase) S88TT14065 (Oxygen) Z711V88R5F (Sarcosine) |
| تواريخ الأحداث: | Date Created: 20150813 Date Completed: 20160512 Latest Revision: 20150812 |
| رمز التحديث: | 20221213 |
| DOI: | 10.1002/cbdv.201400362 |
| PMID: | 26265568 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1612-1880 |
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| DOI: | 10.1002/cbdv.201400362 |