2 research outputs found
Gauging the Flexibility of the Active Site in Soybean Lipoxygenase‑1 (SLO-1) through an Atom-Centered Density Matrix Propagation (ADMP) Treatment That Facilitates the Sampling of Rare Events
We present a computational methodology to sample rare
events in large biological enzymes that may involve electronically
polarizing, reactive processes. The approach includes simultaneous
dynamical treatment of electronic and nuclear degrees of freedom,
where contributions from the electronic portion are computed using
hybrid density functional theory and the computational costs are reduced
through a hybrid quantum mechanics/molecular mechanics (QM/MM) treatment.
Thus, the paper involves a QM/MM dynamical treatment of rare events.
The method is applied to probe the effect of the active site elements
on the critical hydrogen transfer step in the soybean lipoxygenase-1
(SLO-1) catalyzed oxidation of linoleic acid. It is found that the
dynamical fluctuations and associated flexibility of the active site
are critical toward maintaining the electrostatics in the regime where
the reactive process can occur smoothly. Physical constraints enforced
to limit the active site flexibility are akin to mutations and, in
the cases studied, have a detrimental effect on the electrostatic
fluctuations, thus adversely affecting the hydrogen transfer process
The Disulfide Bonds within BST‑2 Enhance Tensile Strength during Viral Tethering
Human
BST-2/tetherin is a host factor that inhibits the release
of enveloped viruses, including HIV-1, HIV-2, and SIV, from the cell
surface by tethering viruses to the host cell membrane. BST-2 has
an α-helical ectodomain that forms disulfide-linked dimers between
two monomers forming a coiled coil. The ectodomain contains three
cysteine residues that can participate in disulfide bond formation
and are critical for viral tethering. The role of the disulfides in
viral tethering is unknown but proposed to be for maintaining the
dimer. We explored the role of the disulfides in the structure of
BST-2 using experimental, biophysical methods. To understand the role
of the disulfides in viral tethering, we used a new approach in viral
tethering, steered molecular dynamics. We find that the disulfides
coordinate the unfolding of the BST-2 monomers, which adds tensile
strength to the coiled coil. Structural differences between oxidized
and reduced BST-2 are apparent during unfolding, showing the monomers
slide past each other in the absence of the disulfides. We found no
evidence to support dissociation of the dimer upon reduction of the
disulfide bonds. Moreover, the structure of BST-2 in the absence of
the disulfides is similar to that of the oxidized form of BST-2, supporting
previous X-ray crystallography and cellular work that showed the disulfides
are not required for expression of BST-2. These data provide new insights
into viral tethering by using novel techniques in the analysis of
BST-2 to give amino acid level insight into functions of BST-2