Atomic and residue hydrophilicity in the context of folded protein structures

Water-protein interactions drive protein folding, stabilize the folded structure, and influence molecular recognition and catalysis. We analyzed the closest protein contacts of 10,837 water molecules in crystallographic structures to define a specific hydrophilicity scale reflecting specific rather than bulk solvent interactions. The tendencies of different atom and residue types to be the nearest protein neighbors of bound water molecules correlated with other hydrophobicity scales, verified the relevance of crystallographically determined water positions, and provided a direct experimental measure of water affinity in the context of the folded protein. This specific hydrophilicity was highly correlated with hydrogen-bonding capacity, and correlated better with experimental than computationally derived measures of partitioning between aqueous and organic phases. Atoms with related chemistry clustered with respect to the number of bound water molecules. Neutral and negatively charged oxygen atoms were the most hydrophilic, followed by positively-charged then neutral nitrogen atoms, followed by carbon and sulfur atoms. Agreement between observed side-chain specific hydrophilicity values and values derived from the atomic hydrophilicity scale showed that hydrophilicity values can be synthesized for different functional groups, such as unusual side or main chains, discontinuous epitopes, and drug molecules. Two methods of atomic hydrophilicity analysis provided a measure of complementarity in the interfaces of trypsin:pancreatic trypsin inhibitor and HIV protease:U-75875 inhibitor complexes. © 1995 Wiley-Liss, Inc.     

Removal of toluene in waste gases using a biological trickling filter

The removal of toluene from waste gas was studied in a trickling biofilter. A high level of water recirculation (4.7 m h^–1) was maintained in order to keep the liquid phase concentration constant and to achieve a high degree of wetting. For loads in the range from 6 to 150 g m^–3 h^–1 the maximum volumetric removal rate (elimination capacity) was 35±10 g m^–3 h^–1, corresponding to a zero order removal rate of 0.11±0.03 g m^–2 h^–1 per unit of nominal surface area. The surface removal was zero order above the liquid phase concentrations of approximately 1.0 g m^–3, corresponding to inlet gas concentrations above 0.7–0.8 g m^–3. Below this concentration the surface removal was roughly of first order. The magnitude of the first order surface removal rate constant, k_1A , was estimated to be 0.08–0.27 m h^–1 (k_1A a=24–86 h^–1). Near-equilibrium conditions existed in the gas effluent, so mass transfer from gas to liquid was obviously relatively fast compared to the biological degradation. An analytical model based on a constant liquid phase concentration through the trickling filter column predicts the effluent gas concentration and the liquid phase concentration for a first and a zero order surface removal. The experimental results were in reasonable agreement with a very simple model valid for conditions with an overall removal governed by the biological degradation and independent of the gas/liquid mass transfer. The overall liquid mass transfer coefficient, K_La, was found to be a factor 6 higher in the system with biofilm compared to the system without. The difference may be explained by: 1. Difference in the wetting of the packing material, 2. Mass transfer occurring directly from the gas phase to the biofilm, and 3. Enlarged contact area between the gas phase and the biofilm due to a rough biofilm surface.     

Surface modification of polymers: chemical, biological and surface analytical challenges

Surface modification methods can optimise the biocompatibility or the specificity of biointeraction of a biosensor or medical device. With only the surface modified, the manufacture and implantation protocol remain unchanged. This review article summarises some of the chemical, surface analytical and biological challenges associated with surface modification of biosensors and biomedical devices.     

沿海防护林体系热效应的遥感分析

沿海防护林体系热效应的遥感分析王述礼,金昌杰,关德新（中国科学院沈阳应用生态研究所１１００１５）ＲｅｍｏｔｅＳｅｎｓｉｎｇＡｎａｌｙｓｉｓｏｎｔｈｅＨｅａｔＥｆｆｅｃｔｓｏｆＣｏａｓｔａｌＳｈｅｌｔｅｒｂｅｌｔＳｙｓｔｅｍ．￥ＷａｎｇＳｈｕｌｉ;Ｊｉ...     

脱落酸对植物线粒体膜生物物理特性的影响

采用１,６－二苯基－１,３,５－已三乙烯（ＤＰＨ）荧光偏振法和中性红法分别研究了脱落酸（ＡＢＡ）对玉米黄化芽及大豆子叶离体线粒体膜的微粘度（η）、表面电位（ψ）等生物物理特性的影响。结果表明：ＡＢＡ有降低线粒体膜的微粘度及提高线粒体膜的表面电位作用,并导致呼吸速率升高,呼吸控制和氧化磷酸化偶联下降。ＡＢＡ对线粒体膜微粘度的作用具有浓度饱和效应;ＡＢＡ对线粒体膜表面电位的提高作用,因植物不同而有差异,对玉米的作用要大于对大豆的。追踪线粒体Ａ（３５０）值的变化,还证实,ＡＢＡ提高了大豆线粒体的Ａ（３５０）值,即导致大豆线粒体的相互聚集（ａｇｇｒｅｇａｔｉｏｎ）。     

Surface immobilization and entrapping of enzymes on glutaraldehyde crosslinked gelatin particles

A mild and reproducible method has been developed for the surface-immobilization of enzymes on glutaraldehyde crosslinked gelatin beads. In this method glutaraldehyde is used in a dual capacity, as crosslinking agent and as the enzyme coupling agent. Glucoamylase (exo-α-1,4-d-glucosidase, EC 3.2.1.3), β-d-fructofuranosidase (invertase, EC 3.2.1.26) and β-d-glucoside (cellobiase, β-d-glucoside glucohydrolase, EC 3.2.1.21) have been successfully immobilized by this method, on the surface of the crosslinked gelatin particles. The method can be combined with the existing technology for the production of gelatin-entrapped enzymes. Thus, dual immobilized enzyme conjugates of glucoamylase and invertase have been prepared using this method, by entrapment of one enzyme in, and surface-binding of the other to, the gelatin matrix. The coupling of glucoamylase onto cross-linked gelatin particles by precipitation with poly(hexamethylenebiguanide hydrochloride) was also tested.     

Charge clusters and the orientation of membrane proteins

Summary Although hydrophobic forces probably dominate in determining whether or not a protein will insert into a membrane, recent studies in our laboratory suggest that electrostatic forces may influence the final orientation of the inserted protein. A negatively charged hepatic receptor protein was found to respond totrans-positive membrane potentials as though electrophoresing into the bilayer. In the presence of ligand, the protein appeared to cross the membrane and expose binding sites on the opposite side. Similarly, a positively charged portion of the peptide melittin crosses a lipid membrane reversibly in response to atrans-negative potential. These findings, and others by Date and co-workers, have led us to postulate that transmembrane proteins would have hydrophobic transmembrane segments bracketed by positively charged residues on the cytoplasmic side and negatively charged residues on the extra-cytoplasmic side. In the thermodynamic sense, these asymmetrically placed charge clusters would create a compelling preference for correct orientation of the protein, given the inside-negative potential of most or all cells. This prediction is borne out by examination of the few transmembrane proteins (glycophorin, M13 coat protein, H-2K^b, HLA-A2, HLA-B7, and mouse Ig heavy chain) for which we have sufficient information on both sequence and orientation.In addition to the usual diffusion and pump potentials measurable with electrodes, the microscopic membrane potential reflects surface charge effects. Asymmetries in surface charge arising from either ionic or lipid asymmetries would be expected to enhance the bias for correct protein orientation, at least with respect to plasma membranes. We introduce a generalized form of Stern equation to assess surface charge and binding effects quantitatively. In the kinetic sense, dipole potentials within the membrane would tend to prevent positively charged residues from crossing the membrane to leave the cytoplasm. These considerations are consistent with the observed protein orientations. Finally, the electrostatic and hydrophobic factors noted here are combined in two hypothetical models of translocation, the first involving initial interaction of the presumptive transmembrane segment with the membrane; the second assuming initial interaction of a leader sequence.     

Ethylene-promoted formation of aerenchyma in seedling roots of Zea mays L. under aerated and non-aerated conditions

The role of ethylene in the formation of lysigenous cortical cavities (aerenchyma) in seedling roots of Zea mays L. cv. Capella, has been studied under aerated and non-aerated conditions. Passing roots from air to aerated water or from an aerated nutrient solution to a non-aerated solution, promoted cavity formation and was accompanied by an increase of the endogenous ethylene concentration. When the endogenous ethylene concentration of roots in aerated nutrient solutions, which otherwise would not produce much cavities, was enhanced by applying ethylene gas (0.1 and 1.0 μl 1^-1 in air) or the ethylene precursor 1-aminocyclopropane-1-car-boxylic acid, cavity formation was promoted. When, on the contrary, the endogenous ethylene concentration of the roots was reduced by adding the inhibitors of ethylene biosynthesis, cobalt ions and aminooxyacetic acid, or when the ethylene action was prevented by silver ions, cavity formation was prevented. It is concluded that endogenous ethylene controls the induction of cavity formation in the roots.     

Surface potential and reaction of the membrane-bound electron transfer components. II. Integrity of the chloroplast membrane and reaction of P-700

Electrostatic characteristics of the membrane surface in the vicinity of P-700 were estimated by analyzing the salt and detergent effects on its reaction rate with ionic reagents using the Gouy-Chapman diffuse double layer theory in various preparations of chloroplasts.

Upon disruption of thylakoid membranes by sonic treatment or by treatment with digitonin, the reaction rate markedly increased, while the estimated surface charge density became smaller.

It was concluded that the membrane surface which determines the reaction rate between P-700 and the ionic reagents changed as the disruption of thylakoid structure. The outer thylakoid surface had more negative charges than the inner one.

Changes in the electrical potential profile across the thylakoid membrane during the illumination were also discussed from these results.