Rong Shen, Wei Han, Giacomo Fiorin, Shahidul M. Islam, Klaus Schulten, and
Benoit Roux.
Structural refinement of proteins by restrained molecular dynamics
simulations with non-interacting molecular fragments.
PLoS Computational Biology, 11:e1004368, 2015.
(19 pages).
(PMC: PMC4624691)
SHEN2015
The knowledge of multiple conformational states is a prerequisite to understand the function
of membrane transport proteins. Unfortunately, the determination of detailed atomic structures
for all these functionally important conformational states with conventional high-resolution
approaches is often difficult and unsuccessful. In some cases, biophysical and
biochemical approaches can provide important complementary structural information that
can be exploited with the help of advanced computational methods to derive structural models
of specific conformational states. In particular, functional and spectroscopic measurements
in combination with site-directed mutations constitute one important source of
information to obtain these mixed-resolution structural models. A very common problem
with this strategy, however, is the difficulty to simultaneously integrate all the information
from multiple independent experiments involving different mutations or chemical labels to
derive a unique structural model consistent with the data. To resolve this issue, a novel
restrained molecular dynamics structural refinement method is developed to simultaneously
incorporate multiple experimentally determined constraints (e.g., engineered metal bridges
or spin-labels), each treated as an individual molecular fragment with all atomic details. The
internal structure of each of the molecular fragments is treated realistically, while there is no
interaction between different molecular fragments to avoid unphysical steric clashes. The
information from all the molecular fragments is exploited simultaneously to constrain the
backbone to refine a three-dimensional model of the conformational state of the protein.
The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of
the Kv1.2 potassium channel in the resting state and by exploring the distance histograms
between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good
agreement with the consensus model of the resting state VSD and the spin-spin distance
histograms from ESR/DEER experiments on T4 lysozyme are accurately reproduced.
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