Liu Ming, Sun TingGuang, Hu JianPing, Chen WeiZu, Wang CunXin
College of Life Sciences and Bioengineering, Beijing University of Technology, Beijing, China.
Biophys Chem. 2008 Jun;135(1-3):19-24. doi: 10.1016/j.bpc.2008.02.017. Epub 2008 Mar 6.
BtuF is the periplasmic binding protein (PBP) that binds vitamin B(12) 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 B(12)-bound BtuF, we investigated the energetics and mechanism of BtuF. A potential of mean force along the postulated vitamin B(12) unbinding pathway was constructed through Jarzynski's equality. The large free energy differences of the postulated B(12) unbinding process suggests the B(12)-bound structure is in a stable closed state and some conformation changes may be necessary to the B(12) unbinding. From the result of the principal component analysis, we found the BtuF-B(12) complex shows clear opening-closing and twisting motion tendencies which may facilitate the unbinding of B(12) 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 B(12) binding pocket, may act as a gate in the B(12) binding and unbinding process.
BtuF是一种周质结合蛋白（PBP），它结合维生素B12并将其递送至ABC转运蛋白BtuCD的周质表面。PBP在配体结合过程中通常会表现出相当大的构象变化，然而，基于晶体结构，BtuF属于一类不会表现出这种行为的PBP亚类。我们对结合了B12的BtuF进行了引导分子动力学研究，以探究BtuF的能量学和机制。通过雅尔津斯基等式构建了沿假定的维生素B12解离途径的平均力势。假定的B12解离过程中存在较大的自由能差异，这表明结合了B12的结构处于稳定的闭合状态，并且B12解离可能需要一些构象变化。从主成分分析结果来看，我们发现BtuF - B12复合物表现出明显的开闭和扭曲运动趋势，这可能有助于B12从结合口袋中解离。我们还探究了BtuF的内在灵活性，结果表明位于B12结合口袋口处的Trp44 - Gln45对可能在B12结合和解离过程中起到门控作用。
