Molecular dynamics hydrophobic surfaces

A crystallographic analysis of xenon binding to [NiFe] hydrogenase, together with a molecular dynamic simulation study of xenon and dihydrogen diffusion in the enzyme interior, suggests the existence of hydrophobic channels connecting the molecular surface with the active site 184). 

It is important to propose molecular and theoretical models to describe the forces, energy, structure and dynamics of water near mineral surfaces. Our understanding of experimental results concerning hydration forces, the hydrophobic effect, swelling, reaction kinetics and adsorption mechanisms in aqueous colloidal systems is rapidly advancing as a result of recent Monte Carlo (MC) and molecular dynamics (MO) models for water properties near model surfaces. This paper reviews the basic MC and MD simulation techniques, compares and contrasts the merits and limitations of various models for water-water interactions and surface-water interactions, and proposes an interaction potential model which would be useful in simulating water near hydrophilic surfaces. In addition, results from selected MC and MD simulations of water near hydrophobic surfaces are discussed in relation to experimental results, to theories of the double layer, and to structural forces in interfacial systems. 

Table V. Results from Selected Molecular Dynamics Studies of Water Near Hydrophobic Surfaces.

Monte Carlo and Molecular Dynamics simulations of water near hydrophobic surfaces have yielded a wealth of information about the structure, thermodynamics and transport properties of interfacial water. In particular, they have demonstrated the presence of molecular layering and density oscillations which extend many Angstroms away from the surfaces. These oscillations have recently been verified experimentally. Ordered dipolar orientations and reduced dipole relaxation times are observed in most of the simulations, indicating that interfacial water is not a uniform dielectric continuum. Reduced dipole relaxation times near the surfaces indicate that interfacial water experiences hindered rotation. The majority of simulation results indicate that water near hydrophobic surfaces exhibits fewer hydrogen bonds than water near the midplane. 

Fig. 8 Proposed model for gramicidin S in a membrane according to the orientational constraints obtained from and N-NMR. The upright backbone alignment (r 80°) and slant of the /3-sheets (p -45°) are compatible with the formation of an oligomeric /3-barrel that is stabilized by hydrogen bonds (dotted lines). A The oligomer is depicted sideways from within the lipid bilayer interior (showing only backbone atoms for clarity, but with hydrophobic side chains added to one of the monomers). Atomic coordinates of GS were taken from a monomeric structure [4], and the two DMPC lipid molecules are drawn to scale (from a molecular dynamics simulation coordinate file). The bilayer cross-section is coloured yellow in its hydrophobic core, red in the amphiphilic regions, and light blue near the aqueous surface. B Illustrates a top view of the putative pore, although the number of monomers remains speculative...

M. Sakurai, H. Tamagawa, K. Ariga, T. Kunitake, Y. Inoue, Molecular Dynamics Simulation of Water between Hydrophobic Surfaces. Implication for the Long-Range Hydrophobic Force , Chem. Phys. Lett, 289, 567 (1998)... 

There are now a wide range of methods available to detect domains with amphipathic helicial characteristics at the residue level. However, new methods for describing the amphipathic nature of protein segments at the atomic level are still under development. Attempts to incorporate atomic hydrophobicity values (Cornette et ai, 1987 Tanford, 1978) in describing the amphipathic nature of peptides or other molecules have been described (Eisenberg and McLachlan, 1986). In the future, however, side-chain flexibility, effective solvent-accessible surfaces, electrostatics, and molecular dynamics will have to be included to obtain an accurate description of the amphipathic nature of these protein fragments at an atomic level. 

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