Tracing conformational changes in proteins.
BACKGROUND
Many proteins undergo extensive conformational changes as part of their functionality. Tracing these changes is important for understanding the way these proteins function. Traditional biophysics-based conformational search methods require a large number of calculations and are hard to apply to large-scale conformational motions.


RESULTS
In this work we investigate the application of a robotics-inspired method, using backbone and limited side chain representation and a coarse grained energy function to trace large-scale conformational motions. We tested the algorithm on four well known medium to large proteins and we show that even with relatively little information we are able to trace low-energy conformational pathways efficiently. The conformational pathways produced by our methods can be further filtered and refined to produce more useful information on the way proteins function under physiological conditions.


CONCLUSIONS
The proposed method effectively captures large-scale conformational changes and produces pathways that are consistent with experimental data and other computational studies. The method represents an important first step towards a larger scale modeling of more complex biological systems.
Haspel
Nurit
N
Department of Computer Science, Rice University, Houston, TX 77005, USA.
Moll
Mark
M
Baker
Matthew L
ML
Chiu
Wah
W
Kavraki
Lydia E
LE
D000263:Adenylate Kinase / Q000737:chemistry; D000465:Algorithms; D001419:Bacteria / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D002352:Carrier Proteins / Q000737:chemistry; D018834:Chaperonin 60 / Q000737:chemistry; D003198:Computer Simulation; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry; D008958:Models, Molecular; D033902:Periplasmic Binding Proteins / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D001426:Bacterial Proteins; D002352:Carrier Proteins; D018834:Chaperonin 60; D029968:Escherichia coli Proteins; D033902:Periplasmic Binding Proteins; D011506:Proteins; C028003:RbsB protein, E coli; C107733:cyanovirin N; D000263:Adenylate Kinase