Study on the Mechanism of the BtuF Periplasmic-binding Protein for Vitamin B12

Liu Ming; Sun TingGuang; Hu JianPing; Chen WeiZu; Wang CunXin

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Study on the Mechanism of the BtuF Periplasmic-binding Protein for Vitamin B12

Liu Ming,Sun TingGuang,Hu JianPing,Chen WeiZu,Wang CunXin * #

College of Life Sciences and Bioengineering, Beijing University of Technology

*Correspondence author

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Funding: 国家自然科学基金,国家自然科学基金,教育部博士点基金（No.30670497,10574009,20040005013）

Opened online: 5 March 2008

Accepted by: none

Citation: Liu Ming,Sun TingGuang,Hu JianPing.Study on the Mechanism of the BtuF Periplasmic-binding Protein for Vitamin B12[OL]. [ 5 March 2008] http://en.paper.edu.cn/en_releasepaper/content/19051

BtuF is the periplasmic binding protein (PBP) that binds vitamin B12 and delivers it to the periplasmic surface of the ABC transporter BtuCD. PBPs generally exhibit considerable conformational changes during ligand binding process, however, BtuF belongs to a subclass of PBPs that, doesn’t show such behavior on the basis of the crystal structures. Employing steered molecular dynamics on the B12-bound BtuF, we investigated the energetics and mechanism of BtuF. A potential of mean force along the postulated vitamin B12 unbinding pathway was constructed through Jarzynski’s equality. The large free energy differences of the postulated B12 unbinding process suggests the B12-bound structure is in a stable closed state and some conformation changes may be necessary to the B12 unbinding. From the result of the principal component analysis, we found the BtuF-B12 complex shows clear opening-closing and twisting motion tendencies which may facilitate the unbinding of B12 from the binding pocket. The intrinsic flexibility of BtuF was also explored, and it’s suggested the Trp44-Gln45 pair, which is situated at the mouth of the B12 binding pocket, may act as a gate in the B12 binding and unbinding process.

Keywords:molecular dynamics simulation; steered molecular dynamics; potential of mean force; Principal Component Analysis; BtuF

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