An extended dead-end elimination algorithm to determine gap-free lists of low energy states.
Proteins are flexible systems and commonly populate several functionally important states. To understand protein function, these states and their energies have to be identified. We introduce an algorithm that allows the determination of a gap-free list of the low energy states. This algorithm is based on the dead-end elimination (DEE) theorem and is termed X-DEE (extended DEE). X-DEE is applicable to discrete systems whose state energy can be formulated as pairwise interaction between sites and their intrinsic energies. In this article, the computational performance of X-DEE is analyzed and discussed. X-DEE is implemented to determine the lowest energy protonation states of proteins, a problem to which DEE has not been applied so far. We use X-DEE to calculate a list of low energy protonation states for two bacteriorhodopsin structures that represent the first proton transfer step of the bacteriorhodopsin photocycle.
Kloppmann
Edda
E
Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, BGI, 95447 Bayreuth, Germany.
Ullmann
G Matthias
GM
Becker
Torsten
T
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D001436:Bacteriorhodopsins / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D015394:Molecular Structure; D011522:Protons; D013816:Thermodynamics
D000596:Amino Acids; D011522:Protons; D001436:Bacteriorhodopsins