Many biomolecules are characterized by surfaces containing extended nonpolar regions, and the aggregation and subsequent removal of such surfaces from water is believed to play a critical role in the biomolecular assembly in cells. A better understanding of the hydrophobic hydration of biomolecules may therefore yield new insights into intracellular assembly. Conventional views hold that the hydration shell of small hydrophobic solutes is clathrate-like, characterized by local cage-like hydrogen-bonding structures and a distinct loss in entropy. The hydration of extended nonpolar planar surfaces, however, appears to involve structures that are orientationally inverted relative to clathrate-like hydration shells, with unsatisfied hydrogen bonds that are directed towards the hydrophobic surface. Here we present computer simulations of the interaction between the polypeptide melittin and water that demonstrate that the two different hydration structures also exist near a biomolecular surface. We find that the two structures are distinguished by a substantial difference in the water-water interaction enthalpy, and that their relative contributions depend strongly on the surface topography of the melittin molecule: clathrate-like structures dominate near convex surface patches, whereas the hydration shell near flat surfaces fluctuates between clathrate-like and less-ordered or inverted structures. The strong influence of surface topography on the structure and free energy of hydrophobic hydration is likely to hold in general, and will be particularly important for the many biomolecules whose surfaces contain convex patches, deep or shallow concave grooves and roughly planar areas.

In Chinese medicine, ginseng (Panax ginseng C.A. Meyer) has long been used as a general tonic or an adaptogen to promote longevity and enhance bodily functions. It has also been claimed to be effective in combating stress, fatigue, oxidants, cancer and diabetes mellitus. Most of the pharmacological actions of ginseng are attributed to one type of its constituents, namely the ginsenosides. In this review, we focus on the recent advances in the study of ginsenosides on angiogenesis which is related to many pathological conditions including tumor progression and cardiovascular dysfunctions. Angiogenesis in the human body is regulated by two sets of counteracting factors, angiogenic stimulators and inhibitors. The 'Yin and Yang' action of ginseng on angiomodulation was paralleled by the experimental data showing angiogenesis was indeed related to the compositional ratio between ginsenosides Rg1 and Rb1. Rg1 was later found to stimulate angiogenesis through augmenting the production of nitric oxide (NO) and vascular endothelial growth factor (VEGF). Mechanistic studies revealed that such responses were mediated through the PI3K→Akt pathway. By means of DNA microarray, a group of genes related to cell adhesion, migration and cytoskeleton were found to be up-regulated in endothelial cells. These gene products may interact in a hierarchical cascade pattern to modulate cell architectural dynamics which is concomitant to the observed phenomena in angiogenesis. By contrast, the anti-tumor and anti-angiogenic effects of ginsenosides (e.g. Rg3 and Rh2) have been demonstrated in various models of tumor and endothelial cells, indicating that ginsenosides with opposing activities are present in ginseng. Ginsenosides and Panax ginseng extracts have been shown to exert protective effects on vascular dysfunctions, such as hypertension, atherosclerotic disorders and ischemic injury. Recent work has demonstrates the target molecules of ginsenosides to be a group of nuclear steroid hormone receptors. These lines of evidence support that the interaction between ginsenosides and various nuclear steroid hormone receptors may explain the diverse pharmacological activities of ginseng. These findings may also lead to development of more efficacious ginseng-derived therapeutics for angiogenesis-related diseases.

We here provide definitive evidence that ginsenosideRg1, the pharmacologically active component of ginseng, is a functional ligand of the glucocorticoid receptor (GR) as determined by fluorescence polarization assay. Rg1 increased the phosphorylation of GR, phosphatidylinositol-3 kinase (PI3K), Akt/PKB and endothelial nitric oxide synthase (eNOS) leading to increase nitric oxide (NO) production in human umbilical vein endothelial cell. Rg1-induced eNOS phosphorylation and NO production were significantly reduced by RU486, LY294,002, or SH-6. Also, knockdown of GR completely eliminated the Rg1-induced NO production. This study revealed that Rg1 can indeed serve as an agonist ligand for GR and the activated GR can induce rapid NO production from eNOS via the non-transcriptional PI3K/Akt pathway.

In this selected literature survey, we have seen that the stabilities of duplexes and triplexes are governed by the vertical base stacking, the horizontal specific base-paired H-bonding and the environmental parameters. The entropic contribution in the solvation/desolvation process is important in driving the aggregation of NA strands and duplex formation, but base stacking and specific H-bonding maintain the helical order. Triplex formation shares most of the physical environmental prerequisites with those of duplex NAs. However, some additional environmental conditions are often needed. Only in low pH solution is the polycytidylic strand protonated and, thus, it is possible for the strand to bind to a G.C duplex sequence to give the C+(G.C) triplex. High ionic strength is often necessary for the screening of inter-phosphate repulsion due to the high linear charge density in triplexes. The presence of specific counterions is important for complexation. In the absence of negative supercoiling, existence of an intramolecular triplex is rare except under very acidic conditions for the formation of C+(G.C)-type intramolecular triplex. As expected, the stabilities of both inter- and intramolecular triplexes increase with sequence length. The thermodynamic principles of helix-coil transition of oligo-duplex may be described by the van't Hoff relationship, which assumes a two-state cooperative melting profile. Thus, the enthalpy, entropy and free energy of transition can be evaluated from the experimental melting curves (e.g. OD, DSC). For polynucleotides, because of the non-two-state nature of transition, the simple van't Hoff relationship is no longer valid, and direct calorimetry is needed to obtain reliable thermodynamic parameters. The pH and salt concentration dependence of duplex stability can be formulated and derived from a van't Hoff equation. Base-stacking patterns are simple in duplexes but not so in triplexes due to the diversity in triplet schemes. The sequence dependence of base stacking for duplexes has been characterized and employed to predict the stability of an arbitrary sequence. In conclusion, the stability of duplex is relatively well-characterized by thermodynamic data in terms of both base stacking and specific H-bonding. Thermodynamic studies of triplexes have been far fewer in number. Oligonucleotides have found application in the detection and localization of a mRNA or its gene, the detection of bacterial or viral sequences, and the inhibition of the translation of mRNA and the transcription and replication of DNA (Englisch and Gauss, 1991). In a different approach, oligonucleotides have been targeted directly to a DNA duplex motif of a gene in order to inhibit the expression at the beginning of the transcriptional process.(ABSTRACT TRUNCATED AT 400 WORDS)

The structure and stability of a DNA triple helix was examined by molecular dynamics (MD) simulation using an all-atom force field. A 1.3 ns simulation was performed on a d(CG*G)7 triple helix in a 1 M saltwater solution. The Ewald method was used to calculate the electrostatic interactions of the system. The behavior of the DNA in the saltwater solution was determined by examining the structure, energetics, and mobility of water and ions in the system. The simulation results for the helical parameters support the validity of a model-built triplex -DNA structure. A low root mean square deviation of the dynamic structure from the initial structure demonstrates the stability of the triplex in the salt solution. The sugar pseudorotation, the backbone conformations, and the average helical parameters suggest that the conformation of strands I and III is strictly neither A-form nor B-form, whereas the conformation of strand II remains near the A-form. A higher mobility of both the cytosine strand and the triplexforming guanine strand and also a longer residence time of water molecules in the spine of hydration were observed and are consistent with available NMR results.

ABSTRACT:The metabolic activation of aristolochic acids (AAs) that have been demonstrated to be mutagenic and carcinogenic was investigated. In vitro metabolism study indicated that AAs were metabolized to N-hydroxyaristolactam, which could be either reduced to aristolactams or rearranged to 7-hydroxyaristolactams via the Bamberger rearrangement. In vivo metabolism study is important because the intermediates (aristolactam-nitriumion) of the nitroreduction process are thought to be responsible for the carcinogenicity of AAs. Liquid chromatography-mass spectrometry and liquid chromatography-tandem mass spectrometry (MS/MS) were applied to the analyses of a series of positional isomers of hydroxyaristolactams in rat urine samples after the in vivo study of AAs. Three hydroxylated metabolites of aristolactam II and two hydroxylated metabolites of aristolactam I were identified. The structures of the positional isomers were elucidated from the interpretation of MS/MS spectra and theoretical calculations. In addition, several new metabolites were detected in the rat urine by high-resolution mass spectrometry and MS/MS, including those from the decarboxylation of AAs and the conjugations of acetylation, glucuronidation, and sulfation of aristolochic acid Ia.

Biomolecular surfaces and interfaces are commonly found with apolar character. The hydrophobic effect thus plays a crucial role in processes involving association with biomolecular surfaces in the cellular environment. By computer simulation, we compared the hydrogen bonding structures and energetics of the proximal hydration shells of the monomer and dimer from a recent study of an extrinsic membrane peptide, melittin. The two peptides were studied in their amphipathic alpha-helical forms, which possess extended hydrophobic surfaces characterized by different topography. The topography of the peptide-water interface was found to be critical in determining the enthalpic nature of hydrophobic hydration. This topographical dependence has far-reaching implications in the regulation of bioactivities in the presence of amphipathicity. This result also engenders reconsideration of the validity of using free energy parameters that depend solely on the chemical nature of constituent moieties in characterizing hydrophobic hydration of proteins and biomolecules in general.

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