16 Mechanical energy,protein motion,and the possible origin of life between mica sheets

The origins of life require reliable energy sources. One feasible energy source has not been considered until recently. This is mechanical energy-work (Hansma, 2010, 2012). The spaces between moving muscovite mica sheets are the environment in which mechanical energy is hypothesized to have been involved in the origins of life. Mechanical energy from moving mica sheets has two main sources: (1) The open-and-shut motions of mica sheets in response to water movements in and out between the sheets, and (2) Thermal cycles of day and night acting on bubble ‘defects’ between mica sheets. This mechanical energy is hypothesized to have been involved in the formation (and breaking) of covalent bonds, the rearrangement of polymers and molecular aggregates, and the budding-off of protocells, in the earliest form of cell division. Furthermore, it is hypothesized that the mechanical energy from mica sheets moving open-and-shut is the source of the common open-and-shut motions of enzymes, originating from a protobiotic era when mechanical energy was plentiful and chemical energy was not yet available.     

Possible origin of life between mica sheets

The mica hypothesis is a new hypothesis about how life might have originated. The mica hypothesis provides simple solutions to many basic questions about the origins of life. In the mica hypothesis, the spaces between mica sheets functioned as the earliest cells. These ‘cells’ between mica sheets are filled with potassium ions, and they provide an environment in which: polymer entropy is low; cyclic wetting and drying can occur; molecules can evolve in isolated spaces and also migrate and ligate to form larger molecules. The mica hypothesis also proposes that mechanical energy (work) is a major energy source that could have been used on many length scales to form covalent bonds, to alter polymer conformations, and to bleb daughter cells off protocells. The mica hypothesis is consistent with many other origins hypotheses, including the RNA, lipid, and metabolic ‘worlds’. Therefore the mica hypothesis has the potential to unify origins hypotheses, such that different molecular components and systems could simultaneously evolve in the spaces between mica sheets.     

Molecular Atomistic Simulations of Clay Swelling in Water Dispersions

An atomistic model has been constructed for a dimeric montmorillonite type clay aggregate. The solid was supposed to be dispersed in water. The surrounding aqueous phase was modified from pure water to either salt or polymer solution, and finally represented by a mixed solution containing electrolytes and polyols. A combined energy minimisation procedure followed by a 100 ps real time molecular dynamic simulation was performed on each amorphous cell modelling the solid dispersion. 3D periodic boundary conditions were established to ensure fluid spatial continuity and the calculations proceeded at room temperature. Sodium, potassium and calcium chlorides were tested as shale swelling inhibition additives. The lower hydration energy cation K⁺ was the most effective swelling inhibitor. The adsorption of poly(propylene glyco)s to the ideal smectite surface was also studied. Their tendency to remain adsorbed was associated with the irreversibility of the polymer adsorption process. The conformational changes obtained for organic molecules were responsible for the final orientation of the clay sheets. So it was possible to conclude from qualitative observations that intramolecular interactions may determine a clay dispersion–agglomeration transition by modifying the system entropy. Finally, it was also concluded that specific combinations of additives could enhance their individual capabilities by synergistic effects, determining the effectiveness for some water-based mud formulations. This revised version was published online in June 2006 with corrections to the Cover Date.     

Studies on Plant Viruses-soil Colloids Interactions

Stability and infectivity of cucumber mosaic virus, strain D (CMV-D), associations with kaolinite and montmorillonite were determined, as affected by: i) nature of clay minerals; ii) nature of clay saturating cations; iii) exposure to dissociating salt solutions (2 M LiCl). Infectivity experiments carried out with sediments following centrifugation of the virus-clay mixtures (sd fractions), showed that, in absence of LiCl, the highest values were obtained with kaolinite, in the order Li⁺= K⁺ > NH₄⁺= Mg⁺⁺ > Na⁺ > Ca⁺⁺ clay saturating cations, ranging between 91 and 30 % of the untreated control, whereas comparable montmorillonite fractions gave infectivity values with all cations about 10–15 % of the control. In presence of 2 M LiCl, montmorillonite preserved infectivity of the same fraction (Lsd fraction), which, in the case of Li⁺- or Ca⁺⁺ -saturated samples, was higher when compared with the corresponding sd values, thus revealing for these cations an amplifying effect on infection. This did not occur with kaolinite which, however, gave a Lsd fraction more infectious than the other clay. The results confirmed that clay minerals preserve infectivity of virus preparations exposed to critical conditions, thus providing an explanation for the persistence in soil of infectivity of viruses which are normally not soil-borne. Under appropriate soil conditions these viruses may form complexes with clay minerals thus retaining an infectivity which may be enhanced by addition of cations as those contained in fertilizers.     

Atomic force microscope investigation of large-circle DNA molecules

A circular bacterial artificial chromosome of 148.9kbp on human chromosome 3 has been extended and fixed on bare mica substrates using a developed fluid capillary flow method in evaporating liquid drops. Extended circular DNA molecules were imaged with an atomic force microscope (AFM) under ambient conditions. The measured total lengths of the whole DNA molecules were in agreement with sequencing analysis data with an error range of +/-3.6%. This work is important groundwork for probing single nucleotide polymorphisms in the human genome, mapping genomic DNA, manipulating biomolecular nanotechnology, and studying the interaction of DNA-protein complexes investigated by AFM.     

Ultra-high resolution imaging of DNA and nucleosomes using non-contact atomic force microscopy

Visualisation of nano-scale biomolecules aids understanding and development in molecular biology and nanotechnology. Detailed structure of nucleosomes adsorbed to mica has been captured in the absence of chemical-anchoring techniques, demonstrating the usefulness of non-contact atomic force microscopy (NC-AFM) for ultra-high resolution biomolecular imaging. NC-AFM offers significant advantages in terms of resolution, speed and ease of sample preparation when compared to techniques such as cryo-electron microscopy and X-ray crystallography. In the absence of chemical modification, detailed structure of DNA deposited on a gold substrate was observed for the first time using NC-AFM, opening up possibilities for investigating the electrical properties of unmodified DNA.     

A simple and effective sample preparation method for atomic force microscopy visualization of individual DNA molecules in situ

A simple, controllable and effective sample preparation method was established for atomic force microscopy (AFM) imaging of individual DNA molecules in aqueous solution. Firstly, magnesium ion (Mg²⁺) at a concentration of 5.0–10.0 mM as a positively charged bridge was transferred onto mica to immobilize DNA molecules. Then Mg²⁺-modified mica was used to investigate DNA molecules in any buffer without magnesium ion by AFM. AFM images demonstrated that DNA molecules can be successfully observed in solution with good resolution, reproducibility, and stability. Further, this DNA sample preparation method makes AFM successful to investigate DNA molecular interaction in situ and DNA/chitosan complex in gene delivery.     

Influence of Montmorillonite on Nucleotide Oligomerization Reactions: A Molecular Dynamics Study

We investigate a proposed origins of life scenario involving the clay montmorillonite and its catalytic role in forming oligonucleotides from activated mononucleotides. Clay and mineral surfaces are important for concentrating the reactants and for promoting nucleotide polymerization reactions. Using classical molecular dynamics methods we provide atomic details of reactant conformations prior to polynucleotide formation, lending insight into previously reported experimental observations of this phenomenon. The simulations clarify the catalytic role of metal ions, demonstrate that reactions leading to correct linkages take place primarily in the interlayer, and explain the observed sequence selectivity in the elongation of the chain. The study comparing reaction probabilities involving L- and D-chiral forms of the reactants has found enhancement of homochiral over heterochiral products when catalyzed by montmorillonite.     

Twisting DNA by salt

The structure and properties of DNA depend on the environment, in particular the ion atmosphere. Here, we investigate how DNA twist -one of the central properties of DNA- changes with concentration and identity of the surrounding ions. To resolve how cations influence the twist, we combine single-molecule magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases monotonously with increasing concentration for all ions investigated. Second, for a given salt concentration, DNA twist strongly depends on cation identity. At 100 mM concentration, DNA twist increases as Na⁺ < K⁺ < Rb⁺ < Ba²⁺ < Li⁺ ≈ Cs⁺ < Sr²⁺ < Mg²⁺ < Ca²⁺. Our molecular dynamics simulations reveal that preferential binding of the cations to the DNA backbone or the nucleobases has opposing effects on DNA twist and provides the microscopic explanation of the observed ion specificity. However, the simulations also reveal shortcomings of existing force field parameters for Cs⁺ and Sr²⁺. The comprehensive view gained from our combined approach provides a foundation for understanding and predicting cation-induced structural changes both in nature and in DNA nanotechnology.     

Ion Selectivity of the KcsA Channel: A Perspective from Multi-Ion Free Energy Landscapes

Potassium (K⁺) channels are specialized membrane proteins that are able to facilitate and regulate the conduction of K⁺ through cell membranes. Comprising five specific cation binding sites (S₀-S₄) formed by the backbone carbonyl groups of conserved residues common to all K⁺ channels, the narrow selectivity filter allows fast conduction of K⁺ while being highly selective for K⁺ over Na⁺. To extend our knowledge of the microscopic mechanism underlying selectivity in K⁺ channels, we characterize the free energy landscapes governing the entry and translocation of a Na⁺ or a K⁺ from the extracellular side into the selectivity filter of KcsA. The entry process of an extracellular ion is examined in the presence of two additional K⁺ in the pore, and the three-ion potential of mean force is computed using extensive all-atom umbrella sampling molecular dynamics simulations. A comparison of the potentials of mean force yields a number of important results. First, the free energy minima corresponding to configurations with extracellular K⁺ or Na⁺ in binding site S₀ or S₁ are similar in depth, suggesting that the thermodynamic selectivity governed by the free energy minima for those two binding sites is insignificant. Second, the free energy barriers between stable multi-ion configurations are generally higher for Na⁺ than for K⁺, implying that the kinetics of ion conduction is slower when a Na⁺ enters the pore. Third, the region corresponding to binding site S₂ near the center of the narrow pore emerges as the most selective for K⁺ over Na⁺. In particular, while there is a stable minimum for K⁺ in site S₂, Na⁺ faces a steep free energy increase with no local free energy well in this region. Lastly, analysis shows that selectivity is not correlated with the overall coordination number of the ion entering the pore, but is predominantly affected by changes in the type of coordinating ligands (carbonyls versus water molecules). These results further highlight the importance of the central region near binding site S₂ in the selectivity filter of K⁺ channels.     

Energy distribution and ion selectivity of the bacterial potassium channel

The ion selectivity of the bacterial potassium channel K_CSA is explained upon comparing the energy characteristics of the interaction of cations (Li⁺, Na⁺, K⁺) with atoms of the selectivity filter of the protein pore. Quantum-chemical calculations reveal a deeper potential well for potassium ions, which accounts for preferred K⁺ permeation. It is shown that the conventional methods with AMBER, CHARMM, OPLS force fields in standard parametrization as well as partial re-parametrization give incorrect estimates of ion energy distribution in the channel.     

Slow vapor‐phase desorption of toluene from several ion‐exchanged montmorillonites

The sorption and desorption of volatile compounds from soils and clays exhibit a wide range of kinetics. While much of the sorptive interaction is very rapid, a certain fraction of volatile compounds that enter soil and clays are only slowly desorbed. It is generally believed that the formation of this recalcitrant or slowly desorbing fraction of volatile organic compounds (VOCs) in soils is due to the diffusion of compounds to poorly accessible sorption sites. However, the exact nature of these sites is in doubt. In montmorillonite, there are two likely possibilities for formation of the recalcitrant fraction: sites between the clay lamella and sites within clay particle aggregates. Because montmorillonite may be an important fraction of many soils, we have explored the formation of slowly desorbing toluene on a montmorillonite clay that was ion exchanged with five different ions (K⁺, Na⁺, Ca²⁺, Mg²⁺, and Fe³⁺) to form mineralogically similar clays with varying interlamellar spacing. The recalcitrant fraction was quantified for varying sorption and desorption times. The type of ion exchanged into the clay appears to have an important influence on the formation of a recalcitrant fraction.     

Adsorption/Desorption of toluene on clay minerals

Adsorption/desorption of toluene on montmorillonite, illite, and kaolinite was studied using the batch equilibrium method. The isotherms measured fit the Freundlich equation (r² >0.95). Montmorillonite adsorbed more toluene than illite or kaolinite; the adsorption of toluene on illite and kaolinite was not significantly different. Adsorption of toluene by montmorillonite showed an exponential increase as the ratio of toluene to clay was increased from 5 to 100. The rate studies showed that 62% of the adsorption was completed within 6 h. A rapid desorption was observed initially, followed by slow desorption after 1 h. The desorption rate decreased as the time of adsorption was increased. Almost all of the adsorbed toluene was extracted with water from the clay when the adsorption time was 0.1 h, but only 61% of the toluene could be desorbed when the adsorption time was 24 h.     

K+ and Na+-Induced Self-Assembly of Telomeric Oligonucleotide d(TTAGGG)n

Abstracts

The telomeric DNA oligomers, d(TTAGGG)_n where n=1, 2, 4, could self-associate into the multi-stranded structures in appropriate condition and exhibited a different CD spectra. The present of Na⁺ was more advantage to facilitate the formation of anti-parallel conformation, but the present of K⁺ enhanced their thermal stability. Spectroscopic analysis of 3, 3′- diethyloxadicarbocyanine (DODC) showed the formation of hairpin quadruplex structures for d(TTAGGG)₂ and d(TTAGGG)₄, but d(TTAGGG) could not. The four-stranded tetraplexes and branched nanowire formed in the present of K⁺ or Na⁺ alone were observed by atomic force microscopy (AFM). The ability to self-assemble of d(TTAGGG)_n into four-stranded tetraplexes and nanowires depends strongly on the number of repeating units and ionic environment. A model to explain how these structures formed is proposed.     

Branched Nanowire Based Guanine Rich Oligonucleotides

Abstract

Self-assembly and aggregation of guanine rich sequences can provide useful insights into DNA nanotechnology and telomeric structure and function. In this paper, we designed a guanine rich sequence d(GGCGTTTTGCGG). We found that it can form stable structure in appropriate condition and it exhibits an anomalous CD spectra. This structures can be imaged in ambient environment with a Nanoscope III AFM (Digital Instruments). We found it forms branch structure and long multistrand DNA nanowire after incubation at 37°C for 612 hours in 25 mM TE (pH=8.0) + 5 mM Mg²⁺ + 50 mM K⁺. The ability to self-assemble into branches and long wires not only clearly demonstrate its potential as scaffold structures for nanotechnology, but also give aids to understand telomeric structure further. We have proposed a model to explain how these structures formed.     

Effect of Ca2+ ions on the adhesion and mechanical properties of adsorbed layers of human osteopontin

Using an atomic force microscope and a surface force apparatus, we measured the surface coverage, adhesion, and mechanical properties of layers of osteopontin (OPN), a phosphoprotein of the human bones, adsorbed on mica. OPN is believed to connect mineralized collagen fibrils of the bone in a matrix that dissipates energy, reducing the risk of fractures. Atomic force microscopy normal force measurements showed large adhesion and energy dissipation upon retraction of the tip, which were due to the breaking of the many OPN-OPN and OPN-mica bonds formed during tip-sample contact. The dissipated energy increased in the presence of Ca²⁺ ions due to the formation of additional OPN-OPN and OPN-mica salt bridges between negative charges. The forces measured by surface force apparatus between two macroscopic mica surfaces were mainly repulsive and became hysteretic only in the presence of Ca²⁺: adsorbed layers underwent an irreversible compaction during compression due to the formation of long-lived calcium salt bridges. This provides an energy storage mechanism, which is complementary to energy dissipation and may be equally relevant to bone recovery after yield. The prevalence of one mechanism or the other appears to depend on the confinement geometry, adsorption protocol, and loading-unloading rates.     

The Persistent Question of Potassium Channel Permeation Mechanisms

Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K⁺ ions in and out of a cell, by employing a carefully designed selectivity filter, evolutionarily conserved from viruses to mammals. The structure of the selectivity filter was determined at atomic resolution by x-ray crystallography, showing a tight coordination of desolvated K⁺ ions by the channel. However, the molecular mechanism of K⁺ ions permeation through potassium channels remains unclear, with structural, functional and computational studies often providing conflicting data and interpretations. In this review, we will present the proposed mechanisms, discuss their origins, and will critically assess them against all available data. General properties shared by all potassium channels are introduced first, followed by the introduction of two main mechanisms of ion permeation: soft and direct knock-on. Then, we will discuss critical computational and experimental studies that shaped the field. We will especially focus on molecular dynamics (MD) simulations, that provided mechanistic and energetic aspects of K⁺ permeation, but at the same time created long-standing controversies. Further challenges and possible solutions are presented as well.     

Molecular docking study of the binding of aminopyridines within the K<Superscript>+</Superscript> channel

We present a molecular docking study aimed to identify the binding site of protonated aminopyridines for the blocking of voltage dependent K⁺ channels. Several active aminopyridines are considered: 2-aminopyridine, 3-aminopyridine, 4-aminopyridine, 3,4-diaminopyridine, and 4-aminoquinoleine. We apply the AutoDock force field with a lamarckian genetic algorithm, using atomic charges for the ligands derived from the electrostatic potential obtained at the B3LYP/cc-pVDZ level. We find a zone in the α-subunit of the K⁺ channel bearing common binding sites. This zone corresponds to five amino acids comprised between residuals Thr107 and Ala111, in the KcsA K⁺ channel (1J95 pdb structure). The 2-aminopyridine, 3-aminopyridine, 4-aminopyridine, and 3,4-diaminopyridine bind to the carboxylic oxygens of Thr107 and Ala111. In all cases aminopyridines are perpendicular to the axis of the pore. 4-aminoquinoleine binds to the carboxylic oxygen of Ala111. Due to its large size, the molecular plane is parallel to the axis of the pore. The charge distributions and the structures of the binding complexes suggest that the interaction is driven by formation of several hydrogen bonds. We find 2-aminopyridine, 3-aminopyridine, 4-aminopyridine, and 3,4-diaminopyridine with similar binding energy. Considering the standard error of the estimate of the AutoDock force field, this energy should lie, as a rough estimation, in the interval 3–7 kcal mol⁻¹. On the other hand, 4-aminoquinoleine seems to have a smaller binding energy. Figure Three-dimensional structure of the complex between 4-AQH⁺ and the binding sites of the K⁺ pore. Only the amino acid sequence from Thr107 to Ala111 is considered. Two different representations are included. In the left, the Thr107 position is marked. The right representation shows the CO oxygens of the peptide bond as spacefilled structures.     

Estimation of the Binding Energy in Random Poly(Butylene terephtalate-co-thiodiethylene terephtalate) Copolyesters/Clay Nanocomposites via Molecular Simulation

Molecular mechanics/dynamics computer simulations are used to explore the atomic scale structure and to predict binding energy values for polymer/clay nanocomposites based on random poly(butylene terephtalate-co-thiodiethylene terephtalate) copolyesters, montmorillonite and several, different organic surfactant. Our results reveal that the energy of binding between the polymeric matrix and the montmorillonite platelet shows a decreasing trend with increasing molecular volume, V, of the organic compounds used as surfactant, and that the substitution of hydrogen atoms with a –SH moiety in the organic molecules results in progressively increasing interaction of the surfactant with the copolymer, as the sulfur-containing comonomer concentration is increased. Finally, under the hypothesis that the clay platelets are uniformly dispersed within the polymer matrix, the pristine clay still yields a high interfacial strength between MMT and copolymers.