Paper Citing NAMD - Abstract
Horejs, C.; Pum, D.; Sleytr, U. B.; Tscheliessnig, R.
Structure prediction of an S-layer protein by the mean force method
JOURNAL OF CHEMICAL PHYSICS, 128 Art. No. 065106, FEB 14 2008
S-layer proteins have a wide range of application potential due to their characteristic features concerning self-assembling, assembling on various surfaces, and forming of isoporous structures with functional groups located on the surface in an identical position and orientation. Although considerable knowledge has been experimentally accumulated on the structure, biochemistry, assemble characteristics, and genetics of S-layer proteins, no structural model at atomic resolution has been available so far. Therefore, neither the overall folding of the S-layer proteins-their tertiary structure-nor the exact amino acid or domain allocations in the lattices are known. In this paper, we describe the tertiary structure prediction for the S-layer protein SbsB from Geobacillus stearothermophilus PV72/p2. This calculation was based on its amino acid sequence using the mean force method (MF method) achieved by performing molecular dynamic simulations. This method includes mainly the thermodynamic aspects of protein folding as well as steric constraints of the amino acids and is therefore independent of experimental structure analysis problems resulting from biochemical properties of the S-layer proteins. Molecular dynamic simulations were performed in vacuum using the simulation software NAMD. The obtained tertiary structure of SbsB was systematically analyzed by using the mean force method, whereas the verification of the structure is based on calculating the global free energy minimum of the whole system. This corresponds to the potential of mean force, which is the thermodynamically most favorable conformation of the protein. Finally, an S-layer lattice was modeled graphically using CINEMA4D and compared with scanning force microscopy data down to a resolution of 1 nm. The results show that this approach leads to a thermodynamically favorable atomic model of the tertiary structure of the protein, which could be verified by both the MF Method and the lattice model. (C) 2008 American Institute of Physics.
