Prospects for tertiary structure prediction of RNA based on secondary structure information

We developed a method, called RNA Assembler using Secondary Structure Information Effectively (RASSIE), for predicting RNA tertiary structures using known secondary structure information. We attempted a fragment assembly-based method that uses a secondary structure-based fragment library. For several typical target structures such as stem-loops, bulge-loops, and 2-way junctions, our method provided numerous good quality candidate structures in less computational time than previously proposed methods. By using a high-resolution potential energy function, we were able to select good predicted structures from candidate structures. This method of efficient conformational search and detailed structure evaluation using high-resolution potential is potentially useful for the tertiary structure prediction of RNA.     

Automated RNA tertiary structure prediction from secondary structure and low‐resolution restraints

A novel protocol for all‐atom RNA tertiary structure prediction is presented that uses restrained molecular mechanics and simulated annealing. The restraints are from secondary structure, covariation analysis, coaxial stacking predictions for helices in junctions, and, when available, cross‐linking data. Results are demonstrated on the Alu domain of the mammalian signal recognition particle RNA, the Saccharomyces cerevisiae phenylalanine tRNA, the hammerhead ribozyme, the hepatitis C virus internal ribosomal entry site, and the P4–P6 domain of the Tetrahymena thermophila group I intron. The predicted structure is selected from a pool of decoy structures with a score that maximizes radius of gyration and base–base contacts, which was empirically found to select higher quality decoys. This simple ab initio approach is sufficient to make good predictions of the structure of RNAs compared to current crystal structures using both root mean square deviation and the accuracy of base–base contacts. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Influence of hydrostatic pressure on water absorption of polyoxymethylene: experiment and molecular dynamics simulation

This work experimentally investigated the influence of hydrostatic pressure on the water absorption of polyoxymethylene, followed by analyzing its micro‐mechanism via molecular dynamics simulation. Tests results show that the polyoxymethylene water absorption decreases with the increase in hydrostatic pressure when the latter is within 0–3.0 MPa; it subsequently increases with the increase in hydrostatic pressure in the range of 3.0–5.0 MPa. Simulation of water molecules diffusion on polyoxymethylene surface shows that water molecules diffuse into polyoxymethylene surface during an equilibration run, and water molecule displacement value of maximum relative concentration gives almost the same characteristics: firstly decreases and then increases with the increase of hydrostatic pressure. Simulation of water molecule diffusion inside polyoxymethylene suggests the following: (i) water molecules vibrate from the interior to the edge of polyoxymethylene cell during the equilibration run, and (ii) water diffusion coefficient in polyoxymethylene gives trend of firstly decreasing and then increasing with the increase of hydrostatic pressure. Copyright © 2016 John Wiley & Sons, Ltd.     

Trimethylamine N-oxide stabilizes RNA tertiary structure and attenuates the denaturating effects of urea

Trimethylamine N-oxide (TMAO) and urea are osmolytes. Osmolytes allow cells to remain viable in harsh or extreme environments. Both TMAO and urea are found in shark and rays at approximate molar ratios of 1:2, respectively. At this ratio TMAO nearly completely counteracts the destabilizing effects that urea has on proteins. We ask whether RNA, which is denatured by urea, is stabilized by TMAO in a manner similar to that seen for proteins. We found that TMAO stabilizes Escherichia coli tRNAfmet tertiary structure and counteracts the denaturing effects of urea at the same ratios found for proteins. Cation binding usually drives RNA tertiary structure formation. These results suggest that tertiary structure stability is not only sensitive to cations but also to the aqueous composition and properties of the solvent. We propose that tertiary structure folding is driven by unfavorable interactions between TMAO and the phosphodiester backbone.     

Effects of hydrostatic pressure on lipid and surfactant phases

In the last years a number of advances have been made in our understanding of the high pressure phase behaviour of lipid and surfactant systems, in particular of phospholipid bilayers which can serve as model biomembrane systems. Hydrostatic pressure has been used as a physical parameter for studying the stability and energetics of lyotropic lipid mesophases, but also because high pressure is an important feature of certain natural membrane environments (e.g. of marine biotopes) and because the high pressure phase behaviour of biomolecules is of biotechnological interest (e.g. for high pressure food processing). It has been demonstrated that temperature and pressure have non-congruent effects on the structural and phase behaviour of these systems. By using the pressure–jump relaxation technique in combination with time-resolved synchrotron X-ray diffraction, the kinetics of different mesophase transformations was also investigated.     

Conformation of p-terphenyl under hydrostatic pressure

The conformation of p-terphenyl (C18H14) and deuterated p-terphenyl (C18D14) has been investigated, using high-pressure infrared spectroscopy at liquid-helium temperatures. First-principles calculations, together with the experimental results, were performed to determine the structure of p-terphenyl in the twisted conformation. At low temperatures and pressures, p-terphenyl belongs to the C2 point group of symmetry. In this configuration, the central ring is twisted with respect to the plane of the outer rings. The symmetry of the molecule is nearly C2h, consistent with previous x-ray diffraction measurements.     

Photopolymerization of diacetylenes under hydrostatic pressure

Photopolymerization of diacetylene-bis (toluenesulfonate) (TS-6) under hydrostatic pressure up to 4 kbar has been studied employing timed-resolved absorption spectroscopy of the trimeric reaction intermediate. Formation of the biradical dimer is a non-thermal process occurring at a rate of 10⁷ s^?1 independent of both temperature and pressure. The rate constant for subsequent monomer addition increases exponentially with pressure delineating existence of a linear relationship between height of the energy barrier and reaction distance which is considered to be the key reaction parameter. Measurement of the photopolymerization yield in TS-6, TS-12 and 4-BCMU under pressure in conjunction with statistical considerations confirm (i) that formation of long chains is limited by preformed short chains and (ii) that in TS-6 and TS-12, yet not in 4-BCMU reaction-induced secondary-chain initiation is important.     

Effect of high hydrostatic pressure on prebiotic peptide synthesis

Here we reported the high hydrostatic pressure, as a key factor of deep-sea environment conditions, promoted the peptide formation and should be considered as one of the significant factors in studying the origin of life.     

Melting of icosahedral nickel clusters under hydrostatic pressure

The thermal stabilities and melting behavior of icosahedral nickel clusters under hydrostatic pressure have been studied by constant‐pressure molecular dynamics simulation. The potential energy and Lindemann index are calculated. The overall melting temperature exhibits a strong dependence on pressure. The Lindemann index of solid structure before melting varies slowly and is almost independent of pressure. However, after the clusters melt completely, the Lindemann index at the overall melting point strongly depends on pressure. The overall melting temperature is found to be increasing nonlinearly with increasing pressure, while the volume change during melting decreases linearly with increasing pressure. Under a high pressure and temperature environment, similar angular distributions were found between liquid and solid structures, indicating the existence of a converging local structure. © 2014 Wiley Periodicals, Inc.     

The dependence of dielectric response of an elastomer on hydrostatic pressure

Dielectric methods have been employed to study the high-pressure behavior of a polyurethane elastomer (Solithane 113) in the vicinity of its α transition. The α-loss peak is shifted to higher temperatures and broadened somewhat with the application of hydrostatic pressure up to 6.4 kbars. The slope of T_α vs. P, or dT_α/dP, obtained at low frequencies was found to be equal to dT_g/dP obtained by a volumetric method. Moreover, it attained a nonzero limiting value at high pressures for each frequency tested (3—30,000 Hz) and the limiting value itself increased with increasing frequency from 10.5°C/kbar at 3 Hz to 18°C/kbar at 30,000 Hz. The activation enthalpy ΔH* was found to be nearly constant over the pressure range tested, but the activation volume ΔV* decreased with increasing pressure. The relation dT_α/dP = T (ΔV*/ΔH*) was shown to hold for the elastomer.     

The effect of hydrostatic pressure on the flow properties of various polymers

A novel device to fit on the exit of the ACER capillary extrusion rheometer has been designed to allow the controlled application of hydrostatic pressure to the body of the fluid under test. The rheological properties of the fluid can be examined over a wide range, ambient to 200MPa. This paper will describe the equipment and the effect of hydrostatic pressure and temperature on the flow properties to the various polymer melts, PC, ABS, PP and HDPE.     

Retrogradation characteristics of high hydrostatic pressure processed corn and wheat starch

High hydrostatic pressure (HHP) has been investigated as an alternative to thermal processing for food preservation. HHP has been known to affect high molecular weight polymers causing phase change. Starch is gelatinized at a pressure on the order of 600–700 MPa, at 25 °C. Gelatinized starch recrystallizes during storage affecting the texture and shelf life of food products. The effect of HHP processing on the crystallization of starches from different botanical origins during storage at 4 and 23 °C was investigated. Crystallization kinetics of HHP treated wheat and corn starch gels were compared using DSC. The effect of crystallization on structure was evaluated in terms of storage modulus. The rate of retrogradation depended on the storage temperature (23 °C and 4 °C) and the botanical origin of the starch. The least crystallization was observed in HHP treated wheat starch stored at 23 °C. The storage modulus increased with crystallization of starch.     

Evidence for a thermodynamically distinct Mg2+ ion associated with formation of an RNA tertiary structure

A folding strategy adopted by some RNAs is to chelate cations in pockets or cavities, where the ions neutralize charge from solvent-inaccessible phosphate. Although such buried Mg(2+)-RNA chelates could be responsible for a significant fraction of the Mg(2+)-dependent stabilization free energy of some RNA tertiary structures, direct measurements have not been feasible because of the difficulty of finding conditions under which the free energy of Mg(2+) chelation is uncoupled from RNA folding and from unfavorable interactions with Mg(2+) ions in other environments. In a 58mer rRNA fragment, we have used a high-affinity thermophilic ribosomal protein to trap the RNA in a structure nearly identical to native; Mg(2+)- and protein-stabilized structures differ in the solvent exposure of a single nucleotide located at the chelation site. Under these conditions, titration of a high affinity chelation site takes place in a micromolar range of Mg(2+) concentration, and is partially resolved from the accumulation of Mg(2+) in the ion atmosphere. From these experiments, we estimate the total and site-specific Mg(2+)-RNA interaction free energies over the range of accessed Mg(2+) concentrations. At 0.1 mM Mg(2+) and 60 mM K(+), specific site binding contributes ～-3 kcal/mol of the total Mg(2+) interaction free energy of ～-13 kcal/mol from all sources; at higher Mg(2+) concentrations the site-binding contribution becomes a smaller proportion of the total (-4.5 vs -33 kcal/mol). Under approximately physiological ionic conditions, the specific binding site will be saturated but will provide only a fraction of the total free energy of Mg(2+)-RNA interactions.     

Theoretical studies of solid bicyclo-HMX: effects of hydrostatic pressure and temperature

On the basis of density functional theory (DFT) and molecular dynamics (MD), the structural, electronic, and mechanical properties of the energetic material bicyclo-HMX have been studied. The crystal structure optimized by the LDA/CA-PZ method compares well with the experimental data. Band structure and density of states calculations indicate that bicyclo-HMX is an insulator with the band gap of ca. 3.4 eV and the N-NO(2) bond is the reaction center. The pressure effect on the bulk structure and properties has been investigated in the range of 0-400 GPa. The crystal structure and electronic character change slightly as the pressure increases from 0 to 10 GPa; when the pressure is over 10 GPa, further increment of the pressure determines significant changes of the structures and large broadening of the electronic bands together with the band gap decreasing sharply. There is a larger compression along the c-axis than along the a- and b-axes. To investigate the influence of temperature on the bulk structure and properties, isothermal-isobaric MD simulations are performed on bicyclo-HMX in the temperature range of 5-400 K. It is found that the increase of temperature does not significantly change the crystal structure. The thermal expansion coefficients calculated for the model indicate anisotropic behavior with slightly larger expansion along the a- and c-axes than along the b-axis.     

Further improvement of hydrostatic pressure sample injection for microchip electrophoresis

Hydrostatic pressure sample injection method is able to minimize the number of electrodes needed for a microchip electrophoresis process; however, it neither can be applied for electrophoretic DNA sizing, nor can be implemented on the widely used single-cross microchip. This paper presents an injector design that makes the hydrostatic pressure sample injection method suitable for DNA sizing. By introducing an assistant channel into the normal double-cross injector, a rugged DNA sample plug suitable for sizing can be successfully formed within the cross area during the sample loading. This paper also demonstrates that the hydrostatic pressure sample injection can be performed in the single-cross microchip by controlling the radial position of the detection point in the separation channel. Rhodamine 123 and its derivative as model sample were successfully separated.     

Electrophoresis at elevated hydrostatic pressure of the multiheme hydroxylamine oxidoreductase

The behavior of the multiheme protein hydroxylamine oxidoreductase (HAO) in polyacrylamide gel electrophoresis was studied at hydrostatic pressures up to 3 kbar at 25 degrees C. Due to the limited working volume of the high pressure vessel, the electrophoresis cells were miniaturized. A microcell which accommodates 6 capillary gel tubes is described. Between 1 bar and 1.5 kbar the enzyme did not undergo structural changes detectable in the gel system. At approximately 2 kbar the active form of the enzyme was partially dissociated. At higher pressures, the enzyme was converted to forms which were irreversibly inactive and had a higher apparent molecular mass, suggesting aggregation or denaturation.     

Wettability determined by capillary rise with pressure increase and hydrostatic effects

Capillary rise is the basis of some methods that are widely applied for the determination of contact angles as well as wettabilities of small particles. The equivalent hydraulic radius r(d) in the Classical Washburn equation is assumed to be particle-specific. But it seems that r(d) is not always constant when the type of liquids is different. The new equation with the pressure increment and the hydrostatic effects are theoretically derived based on the Washburn equation, so contact angles of small particles can be measured experimentally independently of r(d). The result shows the validity of the proposed method, and therefore, it becomes possible to accurately measure the wettability of small particles.