Nanoscale dewetting transition in protein complex folding

Instantaneous liquid interfaces

We describe and illustrate a simple procedure for identifying a liquid interface from atomic coordinates. In particular, a coarse-grained density field is constructed, and the interface is defined as a constant density surface for this coarse-grained field. In applications to a molecular dynamics simulation of liquid water, it is shown that this procedure provides instructive and useful pictures of liquid-vapor interfaces and of liquid-protein interfaces.

Cause and effect of melittin-induced pore formation: a computational approach

Melittin embedded in a palmitoyl oleyl phosphatidylcholine bilayer at a high peptide/lipid ratio (1:30) was simulated in the presence of explicit water and ions. The simulation results indicate the incipience of an ion-permeable water pore through collective membrane perturbation by bound peptides. The positively charged residues of melittin not only act as "anchors" but also disrupt the membrane, leading to cell lysis. A detailed analysis of the lipid tail order parameter profile depicts localized membrane perturbation. The lipids in the vicinity of the aqueous cavity adopt a tilted conformation, which allows local bilayer thinning. The prepore thus formed can be considered as the melittin-induced structural defects in the bilayer membrane. Because of the strong cationic nature, the melittin-induced prepore exhibits selectivity toward anions over cations. As Cl(-) ions entered into the prepore, they are electrostatically entrapped by positively charged residues located at its wall. The confined motion of the Cl(-) ions in the membrane interior is obvious from calculated diffusion coefficients. Moreover, reorientation of the local lipids occurs in such a way that few lipid heads along with peptide helices can line the surface of the penetrating aqueous phase. The flipping of lipids argued in favor of melittin-induced toroidal pore over a barrel-stave mechanism. Thus, our result provides atomistic level details of the mechanism of membrane disruption by antimicrobial peptide melittin.

Enhanced surface hydrophobicity by coupling of surface polarity and topography

We use atomistic computer simulation to explore the relationship between mesoscopic (liquid drop contact angle) and microscopic (surface atomic polarity) characteristics for water in contact with a model solid surface based on the structure of silica. We vary both the magnitude and direction of the solid surface polarity at the atomic scale and characterize the response of an aqueous interface in terms of the solvent molecular organization and contact angle. We show that when the topography and polarity of the surface act in concert with the asymmetric charge distribution of water, the hydrophobicity varies substantially and, further, can be maximal for a surface with significant polarity. The results suggest that patterning of a surface on several length scales, from atomic to mum lengths, can make important independent contributions to macroscopic hydrophobicity.

Microscopic wetting of mixed self-assembled monolayers: a molecular dynamics study

Molecular dynamics simulations are used to study the evolution of the organization of water molecules on the flat surface of well-ordered self-assembled monolayers (SAMs) of eight-carbon alkanethiolate chains bound to a gold substrate, as the character of the surface is finely tuned from completely hydrophobic to completely hydrophilic, and as the level of hydration is increased from submonolayer to the equivalent of about two monolayers of water. The hydrophilicity of the SAM surfaces is increased by randomly replacing methyl-terminated alkanethiolate chains with carboxylic acid-terminated chains. We report on the evolution of the structure of the surfaces of the SAMs, both in the absence and presence of water, and the organization of water molecules and the extent of wetting of the surfaces, as the fraction of hydrophilic groups is increased. The results suggest that on the flat organic surfaces with a small fraction of the hydrophilic components the hydrophilic spots serve as nucleation sites, resulting in the growth of a larger number of (smaller) water droplets compared to the completely hydrophobic surface, whereas on the surfaces with a large fraction of the hydrophilic component the uptake of water proceeds via a water film growing, at first, over the hydrophilic domains and, eventually, bridging over the hydrophobic patches, and spreading out over the entire surface. We discuss the implications of these processes on the properties of the organic aerosols in the atmosphere.

Dewetting and hydrophobic interaction in physical and biological systems

Hydrophobicity manifests itself differently on large and small length scales. This review focuses on large-length-scale hydrophobicity, particularly on dewetting at single hydrophobic surfaces and drying in regions bounded on two or more sides by hydrophobic surfaces. We review applicable theories, simulations, and experiments pertaining to large-scale hydrophobicity in physical and biomolecular systems and clarify some of the critical issues pertaining to this subject. Given space constraints, we cannot review all the significant and interesting work in this active field.

Role of water in mediating the assembly of Alzheimer amyloid-beta Abeta16-22 protofilaments

The role of water in promoting the formation of protofilaments (the basic building blocks of amyloid fibrils) is investigated using fully atomic molecular dynamics simulations. Our model protofilament consists of two parallel beta-sheets of Alzheimer Amyloid-beta 16-22 peptides (Ac-K(16)-L(17)-V(18)-F(19)-F(20)-A(21)-E(22)-NH2). Each sheet presents a distinct hydrophobic and hydrophilic face and together self-assemble to a stable protofilament with a core consisting of purely hydrophobic residues (L(17), F(19), A(21)), with the two charged residues (K(16), E(22)) pointing to the solvent. Our simulations reveal a subtle interplay between a water mediated assembly and one driven by favorable energetic interactions between specific residues forming the interior of the protofilament. A dewetting transition, in which water expulsion precedes hydrophobic collapse, is observed for some, but not all molecular dynamics trajectories. In the trajectories in which no dewetting is observed, water expulsion and hydrophobic collapse occur simultaneously, with protofilament assembly driven by direct interactions between the hydrophobic side chains of the peptides (particularly between F-F residues). For those same trajectories, a small increase in the temperature of the simulation (on the order of 20 K) or a modest reduction in the peptide-water van der Waals attraction (on the order of 10%) is sufficient to induce a dewetting transition, suggesting that the existence of a dewetting transition in simulation might be sensitive to the details of the force field parametrization.

Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect

To shed light on the driving force for the hydrophobic effect that partitions amphiphilic lipoproteins between water and membrane, we carried out an atomically detailed thermodynamic analysis of a triply lipid modified H-ras heptapeptide anchor (ANCH) in water and in a DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) bilayer. Combining molecular mechanical and continuum solvent approaches with an improved technique for solute entropy calculation, we obtained an overall transfer free energy of approximately -13 kcal mol(-1). This value is in qualitative agreement with free energy changes derived from a potential of mean force calculation and indirect experimental observations. Changes in free energies of solvation and ANCH conformational reorganization are unfavorable, whereas ANCH-DMPC interactions-especially van der Waals-favor insertion. These results are consistent with an enthalpy-driven hydrophobic effect, in accord with earlier calorimetric data on the membrane partition of other amphiphiles. Furthermore, structural and entropic analysis of molecular dynamics-generated ensembles suggests that conformational selection may play a hitherto unappreciated role in membrane insertion of lipid-modified peptides and proteins.

Hydrophobicity of protein surfaces: Separating geometry from chemistry

To better understand the role of surface chemical heterogeneity in natural nanoscale hydration, we study via molecular dynamics simulation the structure and thermodynamics of water confined between two protein-like surfaces. Each surface is constructed to have interactions with water corresponding to those of the putative hydrophobic surface of a melittin dimer, but is flattened rather than having its native "cupped" configuration. Furthermore, peripheral charged groups are removed. Thus, the role of a rough surface topography is removed, and results can be productively compared with those previously observed for idealized, atomically smooth hydrophilic and hydrophobic flat surfaces. The results indicate that the protein surface is less hydrophobic than the idealized counterpart. The density and compressibility of water adjacent to a melittin dimer is intermediate between that observed adjacent to idealized hydrophobic or hydrophilic surfaces. We find that solvent evacuation of the hydrophobic gap (cavitation) between dimers is observed when the gap has closed to sterically permit a single water layer. This cavitation occurs at smaller pressures and separations than in the case of idealized hydrophobic flat surfaces. The vapor phase between the melittin dimers occupies a much smaller lateral region than in the case of the idealized surfaces; cavitation is localized in a narrow central region between the dimers, where an apolar amino acid is located. When that amino acid is replaced by a polar residue, cavitation is no longer observed.