| Tryptophanyl-tRNA synthetase (TrpRS) catalyzes tryptophan
activation by ATP and its subsequent aminoacylation to tRNA. The structures
of TrpRS have been solved in both open and closed states. They provide
evidence for major ligand-dependent domain motion both in solution and
in crystals. It is of great interest to understand such motion and relate
them to the function of the protein. Our first step is to determine which
torsional angles contribute significantly to the final motion. Our current
method consists of the following steps:
- Estimate the noise level and select a window size s.
- Compute the difference between all contiguous fragments
of length s along the amino-acid chain.
- Threshold by hysteresis to locate large changes and
break the chain into quasi-rigid sub-chains.
- Further break the sub-chains using bisection until each
sub-chain is rigid according to a threshold.
We are testing our method on several proteins, in addition
to TrpRS, that are interesting structurally and functionally.
Once the torsional degrees of freedom are located,
we construct plausible motion pathways between different protein conformations.
Molecular dynamics simulation and normal mode analysis are two main approaches
in the literature for this purpose, but we believe that the probabilistic
roadmap method for motion planning, developed in the robotics community,
will be more useful. The goal of motion planning is to compute obstacle-avoiding
motion for objects with many degrees of freedom. In our problem, the moving
object is a protein with selected torsional angles. High-energy states
of the protein are unfavorable and can be regarded as obstacles. A key
insight from the roadmap method is that the connectivity of the space
can be effectively captured in a graph whose nodes represent randomly
sampled object configurations and edges represent obstacle-avoiding transitions.
As we modify the roadmap method to reflect the characteristics and protein
motion and devise a sampling scheme that takes into account the energy
of different protein conformations, we hope to elucidate the motion pathway
of TrpRS.
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