Macromolecular surface

Macromolecular Surface Films, Charged Films, and Langmuir-Blodgett Layers... 

By covalently attaching reactive groups to a polyelectrolyte main chain the uncertainty as to the location of the associated reactive groups can be eliminated. The location at which the reactive groups experience the macromolecular environment critically controls the reaction rate. If a reactive group is covalently bonded to a macromolecular surface, its reactivity would be markedly influenced by interfacial effects at the boundary between the polymer skeleton and the water phase. Those effects may vary with such factors as local electrostatic potential, local polarity, local hydrophobicity, and local viscosity. The values of these local parameters should be different from those in the bulk phase. 

This bimodal dynamics of hydration water is intriguing. A model based on dynamic equilibrium between quasi-bound and free water molecules on the surface of biomolecules (or self-assembly) predicts that the orientational relaxation at a macromolecular surface should indeed be biexponential, with a fast time component (few ps) nearly equal to that of the free water while the long time component is equal to the inverse of the rate of bound to free transition [4], In order to gain an in depth understanding of hydration dynamics, we have carried out detailed atomistic molecular dynamics (MD) simulation studies of water dynamics at the surface of an anionic micelle of cesium perfluorooctanoate (CsPFO), a cationic micelle of cetyl trimethy-lainmonium bromide (CTAB), and also at the surface of a small protein (enterotoxin) using classical, non-polarizable force fields. In particular we have studied the hydrogen bond lifetime dynamics, rotational and dielectric relaxation, translational diffusion and vibrational dynamics of the surface water molecules. In this article we discuss the water dynamics at the surface of CsPFO and of enterotoxin. 

DNA mediated photoelectron transfer reactions have been demonstrated60 . Binding to DNA assists the electron transfer between the metal-centered donor-acceptor pairs. The increase in rate in the presence of DNA illustrates that reactions at a macromolecular surface may be faster than those in bulk homogeneous phase. These systems can provide models for the diffusion of molecules bound on biological macromolecular surfaces, for protein diffusion along DNA helices, and in considering the effect of medium, orientation and diffusion on electron transfer on macromolecular surfaces. 

Figure 2 The distance dependence characterizing exclusion of small solutes from macromolecular surfaces follows the same exponential behavior as the hydration force between macromolecules. The extent of exclusion can be extracted from the dependence of forces on solute concentration. ITexcess is the effective osmotic pressure applied by the solute in the bulk solution on the macromolecular phase, and np is the maximal pressure from complete exclusion, riexcess/rio = 1 then corresponds to complete exclusion and n excess/Ho = 0 means no inclusion or exclusion. The distance dependent exclusion the polar polyols adonitol (A) and glycerol ( ) from hydrophobically modified hydroxypropyl cellulose (FIPC) and of the nonpolar alcohols i-propanol ( ) and methyl pentanediol (MPD) ( ) from spermidine +-DNA is shown. As in Fig. 1, interaxial spacings are converted to surface separations. The apparent exponential decay length varies between 3.5 and 4 A (solid lines indicate fits to the data).

Surface representations. Often, the interactions between macromolecules take place exclusively at their surfaces. Surface representations have been developed to better visualize macromolecular surfaces. These representations display the overall shapes of macromolecules and can be shaded or colored to indicate particular features such as surface topography or the distribution of electric charges. 

An extreme example of the different appearance of a macromolecular surface to an interacting external environment is provided by polyacryl-... 

Evidence continues to support the explanation of en/.yme catalysis on the basis of the active site (reactive center) of amino acid residues, which is considered to be that relatively small region of the en/yme s macromolecular surface involved in catalysis. Within this site, the enzyme has. strategically positioned functional groups (frnm the side chains of amino acid units) that participate cooperatively in the catalytic action." ... 

Water associated at the interfaces and with macromolecular components may have quite different properties from those in the bulk phase. Water can be expected to form locally ordered structures at the surface of water-soluble, as well as water-insoluble, macromolecules and at the boundaries of the cellular organelles. Biomacromolecules generally have many ionized and polar groups on their surfaces and tend to align near polar water molecules. This ordering effect exerted by the macromolecular surface extends quite far into the surrounding medium. 

Connolly (43,44) and Richmond (45) also developed analytical methods for calculating molecular surface area and volume, which provide nearly exact values for the surface area and enclosed volume. Richmond s method provides analytical derivatives for surface area with respect to the cartesian coordinates of the atoms, which may be useful for docking (Section V). Connolly s algorithm also produces spectacular shaded raster graphics images (46), which give a very different feel for a macromolecular surface than conventional space-filling displays. 

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