A study of the dielectric properties of E. coli ribosomal RNA and proteins in solution

Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel

The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form α-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling α-helix formation, which causes the elongation arrest.

A Review: Origins of the Dielectric Properties of Proteins and Potential Development as Bio-Sensors

Polymers can be classified as synthetic polymers and natural polymers, and are often characterized by their most typical functions namely their high mechanical resistivity, electrical conductivity and dielectric properties. This bibliography report consists in: (i) Defining the origins of the dielectric properties of natural polymers by reviewing proteins. Despite their complex molecular chains, proteins present several points of interest, particularly, their charge content conferring their electrical and dielectric properties; (ii) Identifying factors influencing the dielectric properties of protein films. The effects of vapors and gases such as water vapor, oxygen, carbon dioxide, ammonia and ethanol on the dielectric properties are put forward; (iii) Finally, potential development of protein films as bio-sensors coated on electronic devices for detection of environmental changes particularly humidity or carbon dioxide content in relation with dielectric properties variations are discussed. As the study of the dielectric properties implies imposing an electric field to the material, it was necessary to evaluate the impact of frequency on the polymers and subsequently on their structure. Characterization techniques, on the one hand dielectric spectroscopy devoted for the determination of the glass transition temperature among others, and on the other hand other techniques such as infra-red spectroscopy for structure characterization as a function of moisture content for instance are also introduced.

Reactions of dipolar bio-molecules in nano-capsules--example of folding-unfolding process

The confinement of chemical reactions in nano-capsules can lead to a dramatic effect on the equilibrium constant of these latter. Indeed, capillary effects due to the curvature and surface energy of nano-capsules can alter in a noticeable way the evolution of reactions occurring within. Nano-encapsulation of bio-materials has attracted lately wide interest from the scientific community because of the great potential of its applications in biomedical areas and targeted therapies. The present paper focuses one's attention on alterations of conformation mechanisms due to extremely confining and interacting solvated dipolar macromolecules at their isoelectric point. As a specific example studied here, the folding-unfolding reaction of proteins (particularly RNase A and creatine kinase CK) is drastically changed when encapsulated in solid inorganic hollow nano-capsules. The effects demonstrated in this work can be extended to a wide variety of nano-encapsulation situations. The design and sizing of nano-capsules can even make use of the effects shown in the present study to achieve better and more effective encapsulation.

Dielectrophoretic manipulation of ribosomal RNA

The manipulation of ribosomal RNA (rRNA) extracted from E. coli cells by dielectrophoresis (DEP) has been demonstrated over the range of 3 kHz-50 MHz using interdigitated microelectrodes. Quantitative measurement using total internal reflection fluorescence microscopy of the time dependent collection indicated a positive DEP response characterized by a plateau between 3 kHz and 1 MHz followed by a decrease in response at higher frequencies. Negative DEP was observed above 9 MHz. The positive DEP response below 1 MHz is described by the Clausius-Mossotti model and corresponds to an induced dipole moment of 3300 D with a polarizability of 7.8×10(-32) F m(2). The negative DEP response above 9 MHz indicates that the rRNA molecules exhibit a net moment of -250 D, to give an effective permittivity value of 78.5 ε(0), close to that of the aqueous suspending medium, and a relatively small surface conductance value of ∼0.1 nS. This suggests that our rRNA samples have a fairly open structure accessible to the surrounding water molecules, with counterions strongly bound to the charged phosphate groups in the rRNA backbone. These results are the first demonstration of DEP for fast capture and release of rRNA units, opening new opportunities for rRNA-based biosensing devices.

Theoretical evaluation of dielectric absorption of microwave energy at the scale of nucleic acids

A theoretical model is proposed for the evaluation of dielectric properties of the cell nucleus between 0.3 and 3 GHz, as a function of its nucleic acids (NA) concentration (CNA). It is based on literature data on dielectric properties of DNA solutions and nucleoplasm. In skeletal muscle cells, the specific absorption rate (SAR) ratio between nucleoplasm and cytoplasm is found to be larger than one for CNA above 30 mg/ml. A nearly linear relationship is found between CNA and this nucleocytoplasmic SAR ratio. Considering the nanoscale of the layer of condensed counterions and bound water molecules at the NA-solution interface, the power absorption per unit volume is evaluated at this precise location. It is found to be between one and two orders of magnitude above that in muscle tissue as a whole. Under realistic microwave (MW) exposure conditions, however, these SAR inhomogeneities do not generate any significant thermal gradient at the scale considered here. Nevertheless, the question arises of a possible biological relevance of nonnegligible and preferential heat production at the location of the cell nucleus and of the NA molecules.

Biophysical study of a molecular intermediate preceding collapse of tight couple and Kaltschmidt-Wittmann ribosomes

In previous works we evidenced, by different biophysical approaches, two levels of structural organization in Escherichia coli ribosomal particles. Thermal treatment up to a defined and non-denaturing temperature causes demolition of only one level of structural complexity. By consequence the ribosomal particle exists in an intermediate state between the native form and the completely collapsed one. In this communication we report on a structural comparison of this intermediate state in Kaltschmidt-Wittmann (LC) and 'tight couple' (TC) ribosomes. Three different biophysical approaches were adopted: dielectric spectroscopy, fluorescence and light scattering. Differential responses to thermal treatment are evidenced in the two ribosomal species. In particular TC show a more compact structure and the overall particle population is more homogeneous than LC in the native state. On the other hand, LC particles after thermal treatment undergo major alterations of geometry and/or phenomena of supra-particle aggregation.

Structural stability of ribosomes subjected to RNase treatment evidenced by dielectric spectroscopy and differential scanning microcalorimetry

Previous studies from our laboratory demonstrated the existence of at least two levels of structural complexity in E. coli 70S ribosomes. Ribosomal RNA seems to be principally involved in the overall stability of these structures. In this paper we present an investigation of ribosomes subjected to treatment with RNase. The study is based on both differential scanning microcalorimetry and dielectric spectroscopy. In the thermograms obtained on treated ribosomes only the low temperature peak of the two typical denaturation events observed in native ribosomes, is promptly eliminated by the enzyme treatment. Dielectric spectroscopy measurements carried out on the same samples indicate an alteration of the dielectric behavior previously shown to consist of two subsequent relaxation processes. In fact, only the low frequency relaxation is affected by the treatment. The second one, observed at higher frequency, remains unaltered. The same effect on the dielectric parameters is observed if the ribosome particles are heated and then cooled prior to measurement. These results are consistent with the idea that two different structures are present within the ribosome. One is very stable and withstands both temperature and RNase treatment while the second is promptly abolished by both treatments. Data presented here strongly suggest that the RNA domains exposed to the solvent play a fundamental role in the stability of the 3-D structure of the ribosome particle.

Differential stability of E. coli ribosomal particles and free RNA towards thermal degradation studied by microcalorimetry

We investigated the thermal degradation of E. coli ribosomes by differential scanning microcalorimetry. The 70S particles show two distinctive and irreversible peaks upon thermal degradation. Free rRNA in solution produces, on the contrary, an unstructured denaturation profile. The thermal analysis of 50S particles shows a profile substantially identical to that observed in 70S, while 30S particles produce an unstructured denaturation pattern. Therefore the thermal behavior of the 70S particle is essentially attributable to the denaturation of the 50S subunit. Our data validate previous observations that the 50S has a more rigid structure as compared to 30S, which behaves as a 'floppy' particle. In addition our data suggest that protein/RNA interactions play a significant role to stabilize three-dimensional structures of the ribosome.