Structure prediction of an S-layer protein by the mean force method

Abstract

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.

Single-molecule Force Spectroscopy Reveals the Individual Mechanical Unfolding Pathways of a Surface Layer Protein

“…␣-helical structures are reported to unfold under the presence of much lower forces than observed in our experiments (34,(77)(78)(79). Therefore, the mechanical stability is likely to arise because of ␤-sheet structures, which are located closer to the C-terminal region where the protein consists of Ig-like and fibronectin type III domains (21). Apparently, a long-range coupling, as reported previously (45), can be also observed for S-layer proteins.…”

“…The dissolved proteins immediately interact to form small oligomers, which provide the nucleation seed for the formation of large layers (19). Recently, a structural model of an S-layer protein, namely the protein SbsB of Geobacillus stearothermophilus pV72/p2 (20) could be determined by means of molecular dynamics simulations and small-angle x-ray scattering (21,22). This S-layer protein is made up of 920 amino acids, has a molecular weight of 98 kDa, and forms two-dimensional layers exhibiting p1 lattice symmetry.…”

“…A schematic of the polyprotein approach is illustrated in Fig. 1A, where the calculated structural model of SbsB is shown (21,22). To address the questions of how and whether the protein is influenced because of ligand binding, identical experiments were performed under the presence of secondary cell wall polymers.…”

Biophysical Methods for the Elucidation of the S-Layer Proteins/Metal Interaction

“…The first structural model of an SLP at atomic resolution was reported in 2008 [104]. In that work, the tertiary structure of the SLP of G. stearothermophilus PV72/p2 was predicted from the amino acid sequence.…”

“…Furthermore, Horejs et al consider that a deeper insight on the location, orientation, and steric accessibility of the SLP binding sites is crucial for the development of other applications of SLPs, including the precipitation of metal ions from solutions [104]. Even when the authors recognize the importance of investigations directed toward the analysis of S-layer binding sites, information about modeling of SLPs is scarce, representing a domain where much work remains to be done.…”