Atomistic simulation of hydrophobin HFBII conformation in aqueous and fluorous media and at the water/ vacuum interface (original) (raw)
Related papers
Molecular Dynamics Study of the Folding of Hydrophobin SC3 at a Hydrophilic/Hydrophobic Interface
Biophysical Journal, 2002
Hydrophobins are fungal proteins that self-assemble at hydrophilic/hydrophobic interfaces into amphipathic membranes. These assemblages are extremely stable and posses the remarkable ability to invert the polarity of the surface on which they are adsorbed. Neither the three-dimensional structure of a hydrophobin nor the mechanism by which they function is known. Nevertheless, there are experimental indications that the self-assembled form of the hydrophobins SC3 and EAS at a water/air interface is rich with -sheet secondary structure. In this paper we report results from molecular dynamics simulations, showing that fully extended SC3 undergoes fast (ϳ100 ns) folding at a water/hexane interface to an elongated planar structure with extensive -sheet secondary elements. Simulations in each of the bulk solvents result in a mainly unstructured globular protein. The dramatic enhancement in secondary structure, whether kinetic or thermodynamic in origin, highlights the role interfaces between phases with large differences in polarity can have on folding. The partitioning of the residue side-chains to one of the two phases can serve as a strong driving force to initiate secondary structure formation. The interactions of the side-chains with the environment at an interface can also stabilize configurations that otherwise would not occur in a homogenous solution.
Molecular dynamics of the “hydrophobic patch” that immobilizes hydrophobin protein HFBII on silicon
Journal of Molecular Modeling, 2010
The experimentally-observed stable, electricallyconducting interface formed between hydrophobin protein HFBII and silicon provides a model system for the Bio/ICT interfaces required for bionanoelectronics. The present work used molecular dynamics (MD) computer simulations to investigate the atom-scale details of the assembly and structure of the HFBII/silicon interface, using models on the order of 40,000 atoms to compute energy profiles for the full protein interacting with a bare Si(111) substrate in aqueous solution. Five nanoseconds of free, equilibrated dynamics were performed for six models with initial protein:silicon separations ranging from 1.2 to 0.2 nanometers in steps of 0.2 nm. Three of the models formed extensive protein:silicon van der Waals's interfacial contacts. The model with 0.2 nm starting separation serves as an illustrative example of the dynamic interface created, whereby hydrophobic patch residues cycle between flat and more protruding patch conformations that favor respectively close inter-patch and close patch-surface contacts, with protein:surface separations cycling between 0.2 and 0.4 nm over the 5 ns of dynamics. Analysis of residue-based binding energies at the interface reveal three leucines Leu19, Leu21 and Leu63, together with isoleucine Ile22 and alanine Ala61, as the primary drivers towards adhesion on bare silicon, providing the atom-scale details of HFBII's hydrophobic patch which in turn provides leads for the engineering of more tightly-coupled interfaces.
Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation
Hydrophobins represent an important group of proteins from both a biological and nanotechnological standpoint. They are the means through which filamentous fungi affect their environment to promote growth, and their properties at interfaces have resulted in numerous applications. In our study we have combined protein docking, molecular dynamics simulation, and electron cryo-microscopy to gain atomistic level insight into the surface structure of films composed of two class II hydrophobins: HFBI and HFBII produced by Trichoderma reesei. Together our results suggest a unit cell composed of six proteins; however, our computational results suggest P6 symmetry, while our experimental results show P3 symmetry with a unit cell size of 56 Å . Our computational results indicate the possibility of an alternate ordering with a three protein unit cell with P3 symmetry and a smaller unit cell size, and we have used a Monte Carlo simulation of a spin model representing the hydrophobin film to show how this alternate metastable structure may play a role in increasing the rate of surface coverage by hydrophobin films, possibly indicating a mechanism of more general significance to both biology and nanotechnology. Citation: Magarkar A, Mele N, Abdel-Rahman N, Butcher S, Torkkeli M, et al. (2014) Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation. PLoS Comput Biol 10(7): e1003745.
Self-assembly of hydrophobin protein rodlets studied with atomic force spectroscopy in dynamic mode
Langmuir, 2011
We have investigated the self-assembling properties of the class I hydrophobin Vmh2 isolated from the fungus Pleurotus ostreatus. Five different hydrophobin self assembled samples including monolayers, bilayers, and rodlets have been prepared by Langmuir technique and studied at the nanoscale. Local wettability and visco-elasticity of the different hydrophobins samples were obtained from atomic force spectroscopy experiments in dynamic mode performed at different, controlled relative humidity (RH) values. It was found that hydrophobins assembled either in rodlets or in bilayer films, display similar hydropathicity and viscoelasticity in contrast to the case of monolayers, whose hydropathicity and viscoelasticity depend on the adopted preparation method (Langmuir−Blodgett or Langmuir−Schaeffer). The comparison with monolayers properties evidences a rearrangement of the bilayers adsorbed onto solid substrates. It is shown that this rearrangement leads to the formation of a stable hydrophobic film, and that the rodlets structure consists in fragments of restructured proteins bilayers. Our results support the hypothesis that the observed variations in the viscoelastic properties could be ascribed to the localization of the large flexible loop, typical of Class I hydrophobins which appears free at the air interface for LB monolayers but not for the other samples. These findings should now serve future developments and applications of hydrophobin films beyond the archetypal monolayer.
Langmuir, 2009
Hydrophobins are a group of surface-active fungal proteins known to adsorb to the air/water interface and selfassemble into highly crystalline films. We characterized the self-assembled protein films of two hydrophobins, HFBI and HFBII from Trichoderma reesei, directly at the air/water interface using Brewster angle microscopy, grazingincidence X-ray diffraction, and reflectivity. Already in zero surface pressure, HFBI and HFBII self-assembled into micrometer-sized rafts containing hexagonally ordered two-dimensional crystallites with lattice constants of 55 Å and 56 Å, respectively. Increasing the pressure did not change the ordering of the proteins in the crystallites. According to the reflectivity measurements, the thicknesses of the hydrophobin films were 28 Å (HFBI) and 24 Å (HFBII) at 20 mN/m. The stable films could also be transferred to a silicon substrate. Modeling of the diffraction data indicated that both hydrophobin films contained six molecules in the unit cell, but the ordering of the molecules was somewhat different for HFBI and HFBII, suggesting specific protein-protein interactions.
Journal of Biological Chemistry, 2007
Hydrophobins are small, amphiphilic proteins secreted by filamentous fungi. Their functionality arises from a patch of hydrophobic residues on the protein surface. Spontaneous selfassembly of hydrophobins leads to the formation of an amphiphilic layer that remarkably reduces the surface tension of water. We have determined by x-ray diffraction two new crystal structures of Trichoderma reesei hydrophobin HFBII in the presence of a detergent. The monoclinic crystal structure (2.2 Å resolution, R ؍ 22, R free ؍ 28) is composed of layers of hydrophobin molecules where the hydrophobic surface areas of the molecules are aligned within the layer. Viewed perpendicular to the aligned hydrophobic surface areas, the molecules in the layer pack together to form six-membered rings, thus leaving small pores in the layer. Similar packing has been observed in the atomic force microscopy images of the self-assembled layers of class II hydrophobin, indicating that the crystal structure resembles that of natural hydrophobin film. The orthorhombic crystal structure (1.0 Å resolution, R ؍ 13, R free ؍ 15) is composed of fiber-like arrays of protein molecules. Rodlet structures have been observed on amphiphilic layers formed by class I hydrophobins; fibrils of class II hydrophobins appear by vigorous shaking. We propose that the structure of the fibrils and/or rodlets is similar to that observed in the crystal structure.
Self-assembled structures of hydrophobins HFBI and HFBII
Journal of Applied Crystallography, 2003
Hydrophobins are small proteins that function in the growth and development of fungi. The structures of class II hydrophobins HFBI and HFBII from Trichoderma reesei were studied using grazing incidence X-ray diffraction. HFBI was weakly ordered but HFBII formed a highly crystalline coating on water surface. Change from monoclinic to hexagonal structure was observed as the sample dried. The threedimensional structures differed from the oblique two-dimensional structures observed in Langmuir-Blodgett monolayers of both HFBI and HFBII by atomic force microscopy.
Journal of Colloid and Interface Science, 2012
The pendant-drop method (with drop-shape analysis) and Langmuir trough are applied to investigate the characteristic relaxation times and elasticity of interfacial layers from the protein HFBII hydrophobin. Such layers undergo a transition from fluid to elastic solid films. The transition is detected as an increase in the error of the fit of the pendant-drop profile by means of the Laplace equation of capillarity. The relaxation of surface tension after interfacial expansion follows an exponential-decay law, which indicates adsorption kinetics under barrier control. The experimental data for the relaxation time suggest that the adsorption rate is determined by the balance of two opposing factors: (i) the barrier to detachment of protein molecules from bulk aggregates and (ii) the attraction of the detached molecules by the adsorption layer due to the hydrophobic surface force. The hydrophobic attraction can explain why a greater surface coverage leads to a faster adsorption. The relaxation of surface tension after interfacial compression follows a different, square-root law. Such behavior can be attributed to surface diffusion of adsorbed protein molecules that are condensing at the periphery of interfacial protein aggregates. The surface dilatational elasticity, E, is determined in experiments on quick expansion or compression of the interfacial protein layers. At lower surface pressures (<11 mN/m) the experiments on expansion, compression and oscillations give close values of E that are increasing with the rise of surface pressure. At higher surface pressures, E exhibits the opposite tendency and the data are scattered. The latter behavior can be explained with a two-dimensional condensation of adsorbed protein molecules at the higher surface pressures. The results could be important for the understanding and control of dynamic processes in foams and emulsions stabilized by hydrophobins, as well as for the modification of solid surfaces by adsorption of such proteins.
Diffusion of hydrophobin proteins in solution and interactions with a graphite surface
BMC biophysics, 2011
Hydrophobins are small proteins produced by filamentous fungi that have a variety of biological functions including coating of spores and surface adhesion. To accomplish these functions, they rely on unique interface-binding properties. Using atomic-detail implicit solvent rigid-body Brownian dynamics simulations, we studied the diffusion of HFBI, a class II hydrophobin from Trichoderma reesei, in aqueous solution in the presence and absence of a graphite surface. In the simulations, HFBI exists in solution as a mixture of monomers in equilibrium with different types of oligomers. The oligomerization state depends on the conformation of HFBI. When a Highly Ordered Pyrolytic Graphite (HOPG) layer is present in the simulated system, HFBI tends to interact with the HOPG layer through a hydrophobic patch on the protein. From the simulations of HFBI solutions, we identify a tetrameric encounter complex stabilized by non-polar interactions between the aliphatic residues in the hydrophobic...