Paper Citing NAMD - Abstract
Liu, Ming; Sun, TingGuang; Hu, JianPing; Chen, WeiZu; Wang, CunXin
Study on the mechanism of the BtuF periplasmic-binding protein for vitamin B-12
BIOPHYSICAL CHEMISTRY, 135:19-24, JUN 2008
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 B12 binding and unbinding process. (c) 2008 Elsevier B.V. All rights reserved.
