Self-Reproduction of Micelles and Liposomes and the Transition to Life

Abstract

Micelles and vesicles (liposomes) are examples of geometrically bounded molecular structures. Conditions have been found under which micelles can be brought to self-reproduction by a simple chemical reaction which takes place at the boundary of the micellar system, at the interface between the micelles' interior and the exterior bulk solvent. During this reaction, the molecules of the boundary are produced which leads to the formation of more micelles as time progresses. The examples are micelles and reverse micelles build by octanoate molecules, and the reactions which lead to self-reproduction are ester hydrolysis or alcohol oxidations.

In another approach, the reproducing micelles are first created chemically by a simple hydrolysis reaction in a two-phase system made of an alkaline aqueous phase and an organic fatty acid ester phase. In an extension of this concept, as upper organic phase octanoic anhydride was used. The initial conditions of the alkaline aqueous phase were so that the pH drop during the reaction led to the formation of vesicles which were able to take up anhydride molecules and to act as a catalyst for the hydrolysis of the remaining anhydride molecules.

The investigation of fatty acid micelles and vesicles is related to the possible role of bounded molecular structures during the early prebiotic evolution on Earth. Because self-reproducing micelles and vesicles can be considered as examples for the chemical version of an autopoietic unit, the requirements of the minimal and universal definition of the living are fulfilled. (According to the definition by Maturana and Varela, an autopoietic unit is a structure which is self-generating and self-perpetuating as a consequence of its own activities within a boundary of its own making).     

High-Throughput Exposure Assessment Tool (HEAT) for exposure-based prioritization of chemicals

Abstract

High-throughput methods are now routinely used to rapidly screen chemicals for potential hazard. However, hazard-based decision-making excludes important exposure considerations resulting in an incomplete estimation of chemical safety. Models to estimate exposure exist, but are generally unsuited to keep up with high-throughput demands. The High-Throughput Exposure Assessment Tool (HEAT) is designed to efficiently predict near-field exposure to consumers and workers via inhalation, oral and dermal routes. HEAT is based on well-known modeling algorithms and provides default model parameters to support reasonably conservative exposure estimates. Underlying chemical-specific data are uploaded or entered by the end user. HEAT’s main strength is the flexible tiered screening functionality, which enables exposure estimates for single or multiple chemicals simultaneously. Hypothetical case examples highlighting the application of HEAT to more complex exposure estimates for alternative and aggregate assessments are provided.     

Homology Modeling of Wild-type,D516V,and H526L Mycobacterium Tuberculosis RNA Polymerase and Their Molecular Docking Study with Inhibitors

Abstract

Rifamicyns (Rifs) are antibiotic widely used for the treatment of tuberculosis (TB); nevertheless, their efficacy has been limited by a high percentage of mutations, principally in the rpoB gene. In this work, the first three-dimensional molecular model of the hypothetical structures for the wild-type and D516V and H526L mutants of Mycobacterium tuberculosis (mtRNAP) were elucidated by a homology modeling method. In addition, the orientations and binding affinities of some Rifs with those new structures were investigated. Our findings could be helpful for the design of new more potent rifamycin analogs.     

Organic biopolymers of venus clams: Collagen-related matrix in the bivalve shells with crossed-lamellar ultrastructure

BackgroundBiochemical studies and spectroscopic techniques have shown that chitin-silk fibroins are common in nacroprismatic bivalve shells. However, the nature of organic biopolymers in the less well studied shell architectures, such as crossed lamellar shells, remain unknown. Here, two venus shells, Callista disrupta and Callista kingii, with crossed lamellar ultrastructure have been studied.MethodsWe employed thermal gravimetric analysis, optical-, confocal- and scanning electron-microscopes, gel-sodium dodecyl sulfate (gel-SDS), FTIR, ultra-performance liquid chromatography and high-performance anion-exchange chromatography system with pulsed amperometric detection to analyse organic macromolecules in the shells.ResultsThermal analysis showed a low concentration of organic macromolecules in C. disrupta (1.38 wt%) and in C. kingii (1.71 wt%). A combination of biochemical protocols, including Calcofluor White staining and FTIR spectroscopic assessment, indicate that amino-polysaccharide chitin together with proteins, are present in the organic scaffolding of the shells. Scanning electron microscope of insoluble acid biopolymer extracts as well as FTIR technique show that the hierarchical structural organizations of organic biopolymers consist collagen-related matrix. Our histochemical fixing and staining techniques reveal many discrete proteins and glycoproteins from soluble organic macromolecules on the gel-SDS. We show here ‘singlet’ and ‘doublet’ glycosaminoglycan bands that are far above 260 kDa.General significance/conclusionsThe presence of collagen matrix in Callista shells shows promise for the new source of biomaterials. Most importantly, the structural organization of the proteinaceous motif is predominantly helical structures and not silk-fibroin unlike in nacreous bivalve shells.     

Chemical Potential,Partial Enthalpy and Partial Volume of Mixtures by NPT Molecular Dynamics

Abstract

Equilibrium NPT molecular dynamics computer simulations have been used to determine the chemical potential, partial enthalpy and partial volume of model Ar-Kr mixtures using newly devised non-intrusive particle insertion and particle swap techniques [P. Sindzingre et al. Chemical Physics, 129 (1989) 213]. In this report we examine, for the first time, in some detail the relative convergence statistics of the particle swap and particle insertion methods for these properties for binary Lennard-Jones (LJ) mixtures. Both species are represented by single-site Lennard-Jones pair potentials with Lorentz-Berthelot rules for the cross-species interactions. We show that, over the whole phase diagram and especially in the vicinity of the fluid-solid coexistence line, the particle swap method gives significantly better statistics than the particle insertion method for the difference in chemical potential of the two species, partial enthalpy and partial volume of each species. Also, we find that, using the particle swap method, the difference in the chemical potential converges more rapidly than the differences in the partial enthalpy and volume.     

Diagnostic use of Molecular Markers In the Evaluation of Thyroid Nodules

ObjectiveTo describe the molecular markers thus far evaluated for use in the care of patients with clinically relevant thyroid nodules.MethodsWe review the currently available molecular tests that have been applied to patients with thyroid nodules.ResultsIn the United States, approximately 450 000 diagnostic fine-needle aspirates will be performed on patients with thyroid nodules this year in an effort to identify thyroid cancer. Unfortunately, this test is imprecise and, at times, inaccurate. Because of this, novel diagnostic testing modalities have been pursued, the most promising of which involve molecular analysis of thyroid tissue. Immunohistochemical staining, analysis for mutations and gene rearrangements, and microarray analysis have all been investigated with regard to their performance characteristics in targeted patient populations.ConclusionsMolecular tests to evaluate thyroid nodules demonstrate variable performance characteristics. Further evaluation of available and emerging molecular tests will necessarily rely on prospective real-world test validation in the clinical setting. (Endocr Pract. 2012;18: 796-802)     

Colleters in Bathysa cuspidata (Rubiaceae): Development,ultrastructure and chemical composition of the secretion

This paper describes the development of colleters of Bathysa cuspidata, Rubiaceae, considering anatomical, histochemical and ultrastructural aspects and going from first differentiation stages until senescence. Further, the chemical composition of the secretion is investigated. The samples were prepared according to the usual techniques for light microscopy and scanning and transmission electron microscopy. Electrophoresis and thin layer chromatography (TLC) were used to confirm the results obtained in the histochemical tests. The colleters occur at the ventral surface of the stipules which protect the leaf primordia as well as the shoot meristem. The origin of the colleters is mixed, involving protoderm and ground meristem. The Bathysa colleters are of the standard type or are bifurcated; this latter type is documented here for the first time for Rubiaceae. Colleter secretion is a mucilage rich in protein, as determined by histochemical tests and confirmed by chemical analysis. Phenolic compounds and terpenes were detected only in the colleters themselves, but not in the secretion. The epithelial cells present conspicuous nuclei and nucleoli and the cytoplasm is rich in dictyosomes, endoplasmic reticulum, mitochondria, vesicles and small vacuoles with a fibrillar content. The accumulation of phenolic compounds and terpenes, the formation of a large central vacuole, the increase of the intercellular and subcuticular spaces occupied by the secretion and, finally, the darkening and the wilting of the colleters characterize the senescence of these structures. The secretion process of the colleters of B. cuspidata suggests a process of programmed cell death.     

Microfluidic Pneumatic Cages: A Novel Approach for In-chip Crystal Trapping,Manipulation and Controlled Chemical Treatment

The precise localization and controlled chemical treatment of structures on a surface are significant challenges for common laboratory technologies. Herein, we introduce a microfluidic-based technology, employing a double-layer microfluidic device, which can trap and localize in situ and ex situ synthesized structures on microfluidic channel surfaces. Crucially, we show how such a device can be used to conduct controlled chemical reactions onto on-chip trapped structures and we demonstrate how the synthetic pathway of a crystalline molecular material and its positioning inside a microfluidic channel can be precisely modified with this technology. This approach provides new opportunities for the controlled assembly of structures on surface and for their subsequent treatment.     

Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine–lysine distances

Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL‐MS), in which protein complexes are crosslinked and characterized using liquid chromatography‐mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine‐reactive N‐hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS³) have a linker arm that is 11.4 Å long when fully extended, allowing C_α (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to ～24 Å apart. However, XL‐MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of ～3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high‐quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine–lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS³, a distance constraint of 26–30 Å between C_α atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL‐MS results to structures or in modeling. We also discuss the comparison of XL‐MS results to MD simulations and known structures as a means to test and validate experimental XL‐MS methods.     

‘Random coil’ 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG

Summary Proton chemical shifts of a series of disordered linear peptides (H-Gly-Gly-X-Gly-Gly-OH, with X being one of the 20 naturally occurring amino acids) have been obtained using 1D and 2D ¹H NMR at pH 5.0 as a function of temperature and solvent composition. The use of 2D methods has allowed some ambiguities in side-chain assignments in previous studies to be resolved. An additional benefit of the temperature data is that they can be used to obtain ‘random coil’ amide proton chemical shifts at any temperature between 278 and 318 K by interpolation. Changes of chemical shift as a function of trifluoroethanol concentration have also been determined at a variety of temperatures for a subset of peptides. Significant changes are found in backbone and side-chain amide proton chemical shifts in these ‘random coil’ peptides with increasing amounts of trifluoroethanol, suggesting that caution is required when interpreting chemical shift changes as a measure of helix formation in peptides in the presence of this solvent. Comparison of the proton chemical shifts obtained here for H-Gly-Gly-X-Gly-Gly-OH with those for H-Gly-Gly-X-Ala-OH [Bundi, A. and Wüthrich, K. (1979) Biopolymers, 18, 285–297] and for Ac-Gly-Gly-X-Ala-Gly-Gly-NH₂ [Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995) J. Biomol. NMR, 5, 67–81] generally shows good agreement for CH protons, but reveals significant variability for NH protons. Amide proton chemical shifts appear to be highly sensitive to local sequence variations and probably also to solution conditions. Caution must therefore be exercised in any structural interpretation based on amide proton chemical shifts.     

Prediction of proton chemical shifts in RNA – Their use in structure refinement and validation

An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct., 76, 81–92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341–346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the ¹H chemical shifts revealing their physical origin. For example, a down-field shift of either H2 or H3 or both indicates a high-syn/syn -angle. In an A-helix it is essentially the 5-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed ¹H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings.     

Structural features of the tmRNA–ribosome interaction

Trans-translation is a process which switches the synthesis of a polypeptide chain encoded by a nonstop messenger RNA to the mRNA-like domain of a transfer-messenger RNA (tmRNA). It is used in bacterial cells for rescuing the ribosomes arrested during translation of damaged mRNA and directing this mRNA and the product polypeptide for degradation. The molecular basis of this process is not well understood. Earlier, we developed an approach that allowed isolation of tmRNA–ribosomal complexes arrested at a desired step of tmRNA passage through the ribosome. We have here exploited it to examine the tmRNA structure using chemical probing and cryo-electron microscopy tomography. Computer modeling has been used to develop a model for spatial organization of the tmRNA inside the ribosome at different stages of trans-translation.     

Recent Advances in Sensing Using Atropoisomeric Molecular Receptors

We describe recent advances in chiroptical chemical sensors, in which the design and implementation is based upon the introduction of atropoisomerically chiral moiety within the molecular skeleton. This report include examples of acyclic, macrocyclic, and polymeric receptors that contain this motif. Although the main applications are in the enantioselective sensing of analytes, we report here some cases where the chiral receptors can in fact be used to senseachiral species. Using circular dichroism (CD) spectroscopy as the technique to detect a receptor–analyte interaction, we can distinguish two main sensor categories: that in which the CD signal of a stereolabile, CD‐silent probe is activated upon binding, and that in which the signal of a CD‐active probe is modulated upon binding. Particular emphasis will be given to cases in which CD spectroscopy is used orthogonally to other means of detection. Chirality 28:116–123, 2016. © 2015 Wiley Periodicals, Inc.     

A Novel Lepidopteran Sex Pheromone Produced by Females of a Lithosiinae Species,Lyclene dharma dharma,in the Family of Arctiidae

Female moths of Lyclene dharma dharma (Arctiidae, Lithosiinae) produced three pheromone components (I–III), which strongly stimulated male antennae. Using GC–MS analysis and chemical derivatizations, the following structures were estimated: 6-methyl-2-octadecanone (I), 14-methyl-2-octadecanone (II), and 6,14-dimethyl-2-octadecanone (III). While the stereochemistry of the chiral centers could not be determined because it was difficult to collect a sufficient amount of the natural pheromone, the plain structures of I and II were confirmed by synthesis of the racemic mixtures starting from diols. These methyl-branched ketones have not been identified as a natural product, indicating that they constitute a new chemical group of lepidopteran female sex pheromones.     

Structural Model of the HIV-1 Tat(46–58)-TAR Complex

Abstract

The trans-activator protein (Tat) of human immunodeficiency virus type 1 (HIV-1>) binds to an uridine-rich bulge of an RNA target (TAR; trans-activation responsive element) predominantly via its basic sequence domain. The structure of the Tat(46–58)-TAR complex has been determined by a novel modeling approach relying on structural information about one crucial arginine residue and crosslink data. The strategy described here solely uses this experimental data without additional “modeling” assumptions about the structure of the complex in order to avoid human bias. Model building was performed in a fashion similar to structure calculations from nuclear magnetic resonance (NMR)-spectroscopic data using restrained molecular dynamics.

The resulting set of structures of Tat(46–58) in its complex with TAR reveals that all models have converged to a common fold, showing a backbone root mean square deviation (RMSD) of 1.36Å. Analysis of the calculated structures suggests that HIV-1 Tat forms a hairpin loop in its complex with TAR that shares striking similarity to the hairpin formed by the structure of the bovine immunodeficiency virus Tat protein after TAR binding as determined by NMR studies. The outlined approach is not limited to the Tat-TAR complex modeling, but is also applicable to all molecular complexes with sufficient biochemical and biophysical data available.     

A Self-Consistent Formulation for Analysis and Generation of Non-Uniform DNA Structures

Abstract

A fully self-consistent formulation is described here for the analysis and generation of base-pairs in non-uniform DNA structures, in terms of various local parameters. It is shown that the internal “wedge parameters” are mathematically related to the parameters describing the base-pair orientation with respect to an external helix axis. Hence any one set of three translation and three rotation parameters are necessary and sufficient to completely describe the relative orientation of the base-pairs comprising a step (or doublet). A general procedure is outlined for obtaining an average or global helix axis from the local helix axes for each step. A graphical representation of the local helix axes in the form of a polar plot is also shown and its application for estimating the curvature of oligonucleotide structures is illustrated, with examples of both A and B type structures.