The structure of intrinsic membrane proteins

Intrinsic membrane proteins are embedded in the lipid bilayer so that the polypeptides come in contact with the non-polar region of the bilayer. There are two major types of intrinsic proteins: those with most of their mass outside the cytoplasm (Type I) and those with most of their mass inside the cytoplasm (Type II). In the latter group are the membrane transport systems. The anion exchange system of the human erythrocyte is a dimer of band 3 polypeptides. These polypeptides span the bilary, have most of their mass in the cytoplasm, and are glycosylated. About 20-25% of the polypeptide, however, is in the bilayer. Arguments are presented to support the view that the intramembrane segments of the protein are alpha-helical and that the major protein-protein interactions between the subunits are in the cytoplasmic portion of the protein.     

Classification for molecular aggregation structure of monolayers on the water surface

The melting temperature, T_m, and the crystalline relaxation temperature, Tα_c, of palmitic acid and dipalmitoyl phosphatidylcholine monolayers on the water surface were evaluated by combination of two kinds of measurements: first, the subphase temperature, T_sp, dependence of the monolayer modulus based on the surface pressure-area (π-A) isotherm and second, the T_sp dependence of the electron diffraction, ED patterns of their monolayers. On the basis of their characteristic temperatures of the monolayers, the aggregation structure of the monolayers which were transferred onto a hydrophilic SiO substrate at various surface pressures and T_sps was investigated by means of transmission electron microscopy. The π-A isotherm for the fatty acid monolayer on the pure water surface represented the aggregating process of isolated domains grown right after spreading a solution on the pure water surface. The fatty acid monolayer on the pure water surface was classified into a crystalline monolayer (T_sp < T_m) and an amorphous one (T_sp > T_m). The crystalline monolayer was further classified into two types; crystalline domains were aligned along their crystallographic axes owing to an induced sintering at the interfacial region among monolayer domains by surface compression (T_sp < Tα_c), while not for T_sp > Tα_c. In the case of the phospholipid monolayer, the monolayer was classified into a compressing crystallized monolayer (T_sp < T_m) and an amorphous one (T_sp > T_m). The compressing crystallized monolayer is a monolayer in which crystallization was gradually induced at plateau region on the π-A isotherm by compression. Electron diffraction studies of arachidic acid monolayers in different dissociated states of hydrophilic groups revealed that formation of the compressing crystallized monolayer was attributed to an electrostatic repulsion among ionic hydrophilic groups. It was concluded that the aggregation structure of monolayers on the water surface was systematically classified into ‘the crystalline monolayer’, ‘the amorphous monolayer’ and ‘the compressing crystallized monolayer’, with respect to thermal and chemical (intermolecular repulsive) factors.     

Molecular structure and OH-stretch spectra of liquid water surface

Molecular dynamics simulations are used to investigate typical coordination shells of molecules in the liquid water surface, for two potential energy surfaces. The major undercoordinated species found in the surface include three-coordinated H2O with either a dangling-H or a dangling-O atom and two-coordinated H2O with one hydrogen bond via H, and another via O. Vibrational signatures of the different coordinations are calculated. The 3400 cm(-1) band in the surface sum frequency generation (SFG) spectrum is assigned to four-coordinated molecules within the surface layer. The low-frequency wing of the OH-stretch band, near 3200 cm(-1) in the SFG spectrum, is proposed to be due to collective excitations of a relatively small number of intermolecularly coupled O-H bond vibrations.     

Formation of ice-like water structure on the surface of an antifreeze protein

Antifreeze proteins (AFPs) are found in different species from polar, alpine, and subarctic regions where they serve to inhibit ice crystal growth by adsorption to ice surfaces. Computational methods have the power to investigate the antifreeze mechanism in atomic detail. Molecular dynamics simulations of water under different conditions have been carried out to test our water model for simulations of biological macromolecules in extreme conditions: very low temperatures (200 K) and at the ice/liquid water interface. We show that the flexible F3C water model reproduces properties of water in the solid phase (ice I(h)), the supercooled liquid phase, and at the ice/liquid water interface. Additionally, the hydration of the type III AFP from ocean pout was studied as a function of temperature. Hydration waters on the ice-binding surface of the AFP were less distorted and more tetrahedral than elsewhere on the surface. More ice-like hydrating water structures formed on the ice-binding surface of the protein such that it created an ice-like structure in water within its first hydration layer but not beyond, suggesting that this portion of the protein has high affinity for ice surfaces.     

Molecular dynamics investigation of the intrinsic structure of water-fluid interfaces via the intrinsic sampling method

Capillary wave fluctuations smooth out the structure of fluid interfaces, making difficult the detailed analysis of the interfacial structure. Most computer simulation investigations performed to date have focused on the computation of average density profiles, ignoring the characterization of the intrinsic structure of the interface. Recent theoretical developments have reversed this situation, making possible the detailed investigation of the interfacial intrinsic structure at an unprecedented level of detail. In this article we investigate via molecular dynamics simulations the intrinsic structure of water-alkane (hexane and dodecane) interfaces. The implementation of the recently introduced, intrinsic sampling method to compute the intrinsic surface of water-fluid interfaces is discussed. We provide quantitative molecular information on the structure, corrugation, and stiffness of the liquid surfaces. The intrinsic structure of water at alkane interfaces is shown to be insensitive to the alkane-chain length, and can be very accurately described by the intrinsic structure of the water free surface.     

Comments on surface structure analysis by water and nitrogen adsorption

Specific surface area and pore size distribution are determined usually from adsorption isotherms at low temperatures using nitrogen or noble gases. These are not absolute parameters and the measuring methods are fraught with serious difficulties. General problems of sorption measurements and recent developments are discussed. To obtain information for practical purposes these measurements need to be supplemented by investigations of the sorbate/sorbent system used in practice. Results of the measurement of nitrogen and water vapour adsorption on different materials are compared. This revised version was published online in July 2006 with corrections to the Cover Date.     

Combined effect of inherent residual chloride and bound water content and surface morphology on the intrinsic electron-transfer activity of ruthenium oxide

Journal of Solid State Electrochemistry - RuO2 is an unparalleled electrode with wider applications. Chloride, bound water, and surface stoichiometry are the inherent residues of RuO2 left upon the...     

Effects of the structure of anionic polyelectrolytes on surface potentials of their aggregates in water

The surface potential, ψ in mV, was determined for the following polyelectrolytes and co-polyelectrolytes in aqueous solution: sodium poly(styrene sulfonate); sodium poly(vinyl sulfonate); poly(vinyl alcohol-co-55% sodium vinyl sulfate); poly(methylmethacrylate-co-40% sodium styrene sulfonate); poly (methylmethacrylate-co-60% sodium styrene sulfonate); poly(styrene-co-56% styrene sulfonate); and poly(styrene-co-80% styrene sulfonate). For comparison, the surface potentials of aqueous sodium dodecyl sulfate and sodium dodecylbenzene sulfonate micelles were also determined. The dyes neutral red and safranine-T were used as indicators. ThepKa of the former was calculated from the Henderson-Hasselbach equation, using UV-VIS spectroscopy to determine the concentration of protonated ground state as a function of pH. The surface potential of the aggregates was culculated from the equation: $$pKa_{\text{i}} = pKa_0 - {{F\Psi } \mathord{\left/ {\vphantom {{F\Psi } {2.3RT}}} \right. \kern-\nulldelimiterspace} {2.3RT}}$$ wherepKa _i andpKa _o refer to the indicatorpKa in the presence of charged and nonionic interfaces, respectively, and the other terms have their usual meaning. The protonation kinetics of the triplet state of safranine-T (measured from the decay of its transient absorption at 830 nm) was used to determine hydronium ion concentrations at aggregate interfaces, and the corresponding surface potentials were calculated from: $$a_{{\text{Hi}}} = a_{{\text{Haq}}} \times \exp \left( {{{ - F\Psi } \mathord{\left/ {\vphantom {{ - F\Psi } {RT}}} \right. \kern-\nulldelimiterspace} {RT}}} \right)$$ wherea _Hi anda _Haq refer to the hydronium ion activity at the aggregate interface, and in bulk water, respectively. Surface potentials determined by both techniques were in excellent agreement. Values of ψ were found to depend on the structure of the polyelectrolyte, sodium poly(styrene sulfonate) versus sodium poly(vinyl sulfonate) and, for the same type of co-polyelectrolyte, on the percentage of charged monomer.     

Effect of surface polarity on water contact angle and interfacial hydration structure

We perform molecular dynamics simulations of water in the presence of hydrophobic/hydrophilic walls at T = 300 K and P = 0 GPa. For the hydrophilic walls, we use a hydroxylated silica model introduced in previous simulations [Lee, S. H.; Rossky, P. J. J. Chem. Phys. 1994, 100, 3334. Giovambattista, N.; Rossky, P. J.; Debenedetti, P. G.; Phys. Rev. E 2006, 73, 041604.]. By rescaling the physical partial atomic charges by a parameter 0 相似文献   

The influence of ions on the structure of water

Journal of Structural Chemistry - The main features of the changes produced by ions in water may be summarized as follows. The influence of ions on the structure of the “free” water...