Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations

An efficient Monte Carlo (MC) algorithm including concerted rotations is directly compared to molecular dynamics (MD) in all-atom statistical mechanics folding simulations of small polypeptides. The previously reported algorithm "concerted rotations with flexible bond angles" (CRA) has been shown to successfully locate the native state of small polypeptides. In this study, the folding of three small polypeptides (trpzip2/H1/Trp-cage) is investigated using MC and MD, for a combined sampling time of approximately 10(11) MC configurations and 8 micros, respectively. Both methods successfully locate the experimentally determined native states of the three systems, but they do so at different speed, with 2-2.5 times faster folding of the MC runs. The comparison reveals that thermodynamic and dynamic properties can reliably be obtained by both and that results from folding simulations do not depend on the algorithm used. Similar to previous comparisons of MC and MD, it is found that one MD integration step of 2 fs corresponds to one MC scan, revealing the good sampling of MC. The simplicity and efficiency of the MC method will enable its future use in folding studies involving larger systems and the combination with replica exchange algorithms.     

Amarisolide monohydrate,a 2‐(β‐glu­cosyl)­neoclerodane

The absolute configuration of the neoclerodane glycoside amarisolide, presented here as the monohydrate, C₂₆H₃₆O₉·H₂O, has been determined by association with the known configuration of the glucose moiety. Its structure was established as 2β‐(O‐β‐d ‐gluco­pyran­osyl)­neocleroda‐3,13(16),14‐trien‐15,16‐epoxy‐18,19‐olide. Extensive hydrogen bonding among the hydroxyl groups of the sugar moiety forms layers which are interconnected by water mol­ecules.     

Design of original bioactive formulations based on sugar-surfactant/non-steroidal anti-inflammatory catanionic self-assemblies: a new way of dermal drug delivery

A new kind of catanionic assembly was developed that associates a sugar-based surfactant with a non-steroidal anti-inflammatory drug (NSAID). Three different assemblies using indomethacin, ibuprofen and ketoprofen as NSAIDs were easily obtained in water by an acid-base reaction. These assemblies formed new amphiphilic entities because of electrostatic and hydrophobic effects in water and led to the spontaneous formation of vesicles. These catanionic vesicles were then tested as potential NSAID delivery systems for dermatological application. The anti-inflammatory activity was evaluated in vivo, and this study clearly showed an improved therapeutic effect for NSAIDs that were formulated as catanionic vesicles. These vesicles ensured a slower diffusion of the NSAID through the skin. This release probably increased the time of retention of the NSAID in the targeted strata of the skin. Thus, the present study suggests that this catanionic bioactive formulation could be a promising dermal delivery system for NSAIDs in the course of skin inflammation treatment.     

BLEACHING OF PURPLE MEMBRANE WITH O-SUBSTITUTED HYDROXYLAMINES

Abstract The retinal Schiff base of bacteriorhodopsin, in the purple membrane from Halobacterium halobium , can be cleaved by hydroxylamine in the presence of light. We have further investigated this reaction with a series of O -substituted hydroxylamines, RONH₂, where R = -H (HA), -CH₃ (MHA), -SO₃− (HAS), benzyl- (BHA), p -nitrobenzyl- (NBHA), and pentafluorobenzyl- (FBHA). All except MHA caused light-induced bleaching of the purple membrane and the chromophore could be regenerated from apomembrane and all- trans retinal. Relative bleaching rate constants were obtained from V = QI _a k ₀ X /( k _r+ k ₀ X ), where V = bleaching rate, Q = quantum yield, I a = absorbed light intensity, X = hydroxylamine concentration, k ₀= rate constant for bleaching and k _r= rate constant for return of photoexcited bacteriorhodopsin to the initial state. This equation fits the time-, concentration- and intensity-dependences of the bleaching reactions in 0.02 M phosphate, pH 7.0. The rate constants k ₀ relative to HA were: MHA: 0; HAS: 0.3; HA: 1.0; BHA: 1.8; FBHA: 10.1; NBHA: 10.8. The relative rate constants do not correlate with the basicity of the derivatives. Instead, the results suggest that the retinal Schiff base is near a non-polar cavity into which an aromatic group can be inserted.     

Analytical potential of a laser ablation–glow discharge–optical emission spectrometry system for the analysis of conducting and insulating materials

The analytical capabilities of a glow discharge (GD) as a secondary source for excitation/ionization of the material provided by laser ablation (LA) have been compared to conventional laser induced breakdown spectroscopy (LIBS). In LA–GD both sources can be independently adjusted to optimize the sampling process and then its subsequent excitation. This could involve a number of analytical performance advantages, such as reduced matrix dependence, greater precision and sensitivity than those encountered in LIBS. For such purpose, an ablation chamber design including two electrodes to generate the GD discharge has been built and assayed. A comparison between LIBS and LA–GD–OES has been carried out, both, under reduced argon and helium atmospheres. Different sets of samples (conducting reference materials, glass and fluorine pellets) have been used to evaluate the novel coupled technique. The LA–GD coupled system has shown to provide lower detection limits. In addition, best linear correlations between intensities and concentrations and lower matrix effects have also been found using the coupled system. Moreover, special advantages of the LA–GD–OES have also been demonstrated for the analysis of fluorine.     

Inclusion complexes of cyclodextrins with 4-amino-1,8-naphthalimides (part 2)

Fluorescence spectroscopy was used to characterize inclusion compounds between 4-amino-1,8-naphthalimides (ANI) derivatives and different cyclodextrins (CDs). The ANI derivatives employed were N-(12-aminododecyl)-4-amino-1,8-naphthalimide (mono-C₁₂ANI) and N,N′-(1,12-dodecanediyl)bis-4-amino-1,8-naphthalimide (bis-C₁₂ANI). The CDs used here were α-CD, β-CD, γ-CD, HP-α-CD, HP-β-CD and HP-γ-CD. The presence of CDs resulted in pronounced blue-shifts in the emission spectra of the ANI derivatives, with increases in emission intensity. This behavior was parallel to that observed for the dyes in apolar solvents, indicating that inclusion complexes were formed between the ANI and the CDs. Mono-C₁₂ANI formed inclusion complexes of 1:1 stoichiometry with all the CDs studied. Complexes with the larger CDs (HP-β-CD, HP-γ-CD and γ-CD) were formed by inclusion of the chromophoric ANI ring system, whereas the smaller CDs (α-CD, HP-α-CD and β-CD) formed complexes with mono-C₁₂ANI by inclusion of the dodecyl chain. Bis-C₁₂ANI formed inclusion complexes of 1:2 stoichiometry with HP-β-CD, HP-γ-CD and γ-CD, but did not form inclusion complexes with α-CD, HP-α-CD and β-CD. The data were treated in the case of the large CDs using a Benesi-Hildebrand like equation, giving the following equilibrium constants: mono-C₁₂ANI:HP-β-CD (K ₁₁ = 50 M^?1), mono-C₁₂ANI:HP-γ-CD (K ₁₁ = 180 M^?1), bis-C₁₂ANI:HP-β-CD (K ₁₂ = 146 M^?2), bis-C₁₂ANI:HP-γ-CD (K ₁₂ = 280 M^?2).     

Generation of new landomycins by combinatorial biosynthetic manipulation of the LndGT4 gene of the landomycin E cluster in S. globisporus

A 3 kb DNA fragment from the Streptomyces globisporus 1912 landomycin E (LaE) biosynthetic gene cluster (lnd) was completely sequenced. Three open reading frames were identified, lndGT4, lndZ4, and lndZ5, whose probable translation products resemble a glycosyltransferase, a reductase, and a hydroxylase, respectively. Studies of generated mutants from disruption and complementation experiments involving the lndGT4 gene allowed us to determine that LndGT4 controls the terminal L-rhodinose sugar attachment during LaE biosynthesis and that LndZ4/LndZ5 are responsible for the unique C11-hydroxylation of the landomycins. Generation of the novel landomycins F, G, and H in the course of these studies provided evidence for the flexibility of lnd glycosyltransferases toward their acceptor substrates and a basis for initial structure-activity relationships within the landomycin family of antibiotics.     

Chemical composition and antibacterial activity of the essential oil of Espeletia nana

The essential oil of the leaves of Espeletia nana Cuatrec., obtained by hydrodistillation, was analyzed by GC-MS, which allowed the identification of 24 components, which made up 99.9% of the oil. The most abundant compounds were a-pinene (38.1%), beta-pinene (17.2%), myrcene (15.0%), spathulenol (4.2%), bicyclogermacrene (4.0%), a-zingiberene (4.0%), and gamma-himachalene (3.7%). Antibacterial activity was tested against Gram-positive and Gram-negative bacteria using the agar disk diffusion method. Activity was observed only against Gram-positive bacteria. MIC values were determined for Staphylococcus aureus ATCC 25923 (200 microg/mL) and Enterococcusfaecalis ATCC 29212 (600 microg/mL).     

Dynamical Aspects of TEM-1 β-Lactamase Probed by Molecular Dynamics

The dynamical aspects of the fully hydrated TEM-1 β-lactamase have been determined by a 5 ns Molecular Dynamics simulation. Starting from the crystallographic coordinates, the protein shows a relaxation in water with an overall root mean square deviation from the crystal structure increasing up to 0.17 nm, within the first nanosecond. Then a plateau is reached and the molecule fluctuates around an equilibrium conformation. The results obtained in the first nanosecond are in agreement with those of a previous simulation (Diaz et al., J. Am. Chem. Soc., (2003) 125, 672–684). The successive equilibrium conformation in solution shows an increased mobility characterized by the following aspects. A flap-like translational motion anchores the Ω-loop to the body of the enzyme. A relevant part of the backbone dynamics implies a rotational motion of one domain relative to the other. The water molecules in the active site can exchange with different residence times. The H-bonding networks formed by the catalytic residues are frequently interrupted by water molecules that could favour proton transfer reactions. An additional simulation, where the aspartyl dyad D214–D233 was considered fully deprotonated, shows that the active site is destabilized.     

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of 4-sulfophenyl isothiocyanate-derivatized peptides on AnchorChip sample supports using the sodium-tolerant matrix 2,4,6-trihydroxyacetophenone and diammonium citrate

The reagent 4-sulfophenyl isothiocyanate (SPITC) is an effective, stable, and inexpensive alternative to commercially available reagents used in the N-terminal sulfonation of peptides for enhanced postsource decay (PSD) in matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOFMS) analyses. However, suppression of ionization of sulfonated peptides due to sample and matrix contaminants such as sodium can be a problem when using prestructured MALDI target sample supports, such as the Bruker Daltonics AnchorChip. We show that use of the salt-tolerant matrix 2,4,6-trihydroxyacetophenone containing diammonium citrate (THAP/DAC) as an alternative to alpha-cyanohydroxycinnamic acid (HCCA) reduces the need for extensive washing of ZipTip-bound peptides or additional on-target sample clean-up steps. Use of the THAP/DAC matrix results in selective ionization of sulfonated peptides with greater peptide coverage, as well as detection of higher mass derivatized peptides, than was observed for HCCA or THAP alone. The THAP/DAC matrix is quite tolerant of sodium contamination, with SPITC-peptides detectable in preparations containing up to 50 mM NaCl. In addition, THAP/DAC matrix was found to promote efficient PSD fragmentation of sulfonated peptides. We demonstrated the utility of using the THAP/DAC MALDI matrix for peptide sequencing with DNA polymerase beta tryptic peptide mixture, as well as tryptic peptides derived from Xiphophorus maculatus brain extract proteins previously separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE).