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Title: Features of Large Hinge-Bending Conformational Transitions.
Prediction of Closed Structure from Open State
Abstract:
We performed a detailed analysis of conformational transition pathways for a
set of ten proteins, which undergo large hinge-bending-type motions with 4-
12 Å RMSD (root mean square distance) between open and closed crystal
structures. ANM-MC algorithm generates a targeted pathway between two
conformations, where the collective modes from the anisotropic network model
(ANM) are used for deformation at each iteration and the conformational
energy of the deformed structure is minimized via a Monte Carlo (MC)
algorithm. The target structure was approached successfully with an RMSD of
0.9-4.1 Å when a relatively low cutoff radius of 10 Å was used
in ANM. Even though one predominant mode (first or second) directed the
open-to-closed conformational transition, changes in the dominant mode
character were observed for most cases along the transition. By imposing
radius of gyration and collectivity constraints during mode selection, it
was possible to predict the cl
osed
structure for eight out of ten proteins (with initial 4.1-7.1 Å and
final 1.7-2.9 Å RMSD to target). Deforming along a single mode leads
to most successful predictions. Based on the previously reported free energy
surface of adenylate kinase, deformations along the first mode produced an
energetically favorable path, which was interestingly facilitated by a
change in mode shape (resembling second and third modes) at key points.
Pathway intermediates are provided in our database of conformational
transitions |
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