Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential.
BACKGROUND
The roughness of energy landscapes is a major obstacle to protein structure prediction, since it forces conformational searches to spend much time struggling to escape numerous traps. Specifically, beta-sheet formation is prone to stray, since many possible combinations of hydrogen bonds are dead ends in terms of beta-sheet assembly. It has been shown that cooperative terms for backbone hydrogen bonds ease this problem by augmenting hydrogen bond patterns that are consistent with beta sheets. Here, we present a novel cooperative hydrogen-bond term that is both effective in promoting beta sheets and computationally efficient. In addition, the new term is differentiable and operates on all-atom protein models.


RESULTS
Energy optimization of poly-alanine chains under the new term led to significantly more beta-sheet content than optimization under a non-cooperative term. Furthermore, the optimized structure included very few non-native patterns.


BACKGROUND
The new term is implemented within the MESHI package and is freely available at http://cs.bgu.ac.il/ approximately meshi.
Levy-Moonshine
Ami
A
Department of Computer Science and Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel.
Amir
El-Ad David
el-AD
Keasar
Chen
C
D003198:Computer Simulation; D030562:Databases, Protein; D006860:Hydrogen Bonding; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins