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Specific ion effects on macromolecular interactions in Escherichia coli extracts.

ABSTRACT: Protein characterization in situ remains a major challenge for protein science. Here, the interactions of ?Tat-GB1 in Escherichia coli cell extracts were investigated by NMR spectroscopy and size exclusion chromatography (SEC). ?Tat-GB1 was found to participate in high molecular weight complexes that remain intact at physiologically-relevant ionic strength. This observation helps to explain why ?Tat-GB1 was not detected by in-cell NMR spectroscopy. Extracts pre-treated with RNase A had a different SEC elution profile indicating that ?Tat-GB1 predominantly interacted with RNA. The roles of biological and laboratory ions in mediating macromolecular interactions were studied. Interestingly, the interactions of ?Tat-GB1 could be disrupted by biologically-relevant multivalent ions. The most effective shielding of interactions occurred in Mg(2+) -containing buffers. Moreover, a combination of RNA digestion and Mg(2+) greatly enhanced the NMR detection of ?Tat-GB1 in cell extracts.

SUBMITTER: Kyne C

PROVIDER: S-EPMC4353357 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

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Specific ion effects on macromolecular interactions in Escherichia coli extracts.

Kyne Ciara C Ruhle Brian B Gautier Virginie W VW Crowley Peter B PB

Protein science : a publication of the Protein Society 20141230 3

Protein characterization in situ remains a major challenge for protein science. Here, the interactions of ΔTat-GB1 in Escherichia coli cell extracts were investigated by NMR spectroscopy and size exclusion chromatography (SEC). ΔTat-GB1 was found to participate in high molecular weight complexes that remain intact at physiologically-relevant ionic strength. This observation helps to explain why ΔTat-GB1 was not detected by in-cell NMR spectroscopy. Extracts pre-treated with RNase A had a differe ...[more]

PMID: 25492389

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Project description:Ion-specific effects in aqueous solution, known as the Hofmeister effect, are prevalent in diverse systems ranging from pure ionic to complex protein solutions. The objective of this paper is to explicitly demonstrate how complex ion-ion and ion-water interactions manifest themselves in the Hofmeister effect based on a series of recent experimental observations. These effects are not considered in the classical descriptions of ion effects, such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, and therefore they fail to describe the origin of the phenomenological Hofmeister effect. However, given that models considering the basic forces of electrostatic and van der Waals interactions can offer rationalization for the core experimental observations, a universal interaction model stands a chance of being developed. In this perspective, we separately derive the contribution from ion-ion electrostatic interactions and ion-water interactions from second harmonic generation (SHG) data at the air-ion solution interface, which yields an estimate of the ion-water interactions in solution. The Hofmeister ion effect observed for biological solutes in solution should be similarly influenced by contributions from ion-ion and ion-water interactions, where the same ion-water interaction parameters derived from SHG data at the air-ion solution interface could be applicable. A key experimental data set available from solution systems to probe ion-water interactions is the modulation of water diffusion dynamics near ions in a bulk ion solution, as well as near biological liposome surfaces. This is obtained from Overhauser dynamic nuclear polarization (ODNP), a nuclear magnetic resonance (NMR) relaxometry technique. The surface water diffusivity is influenced by the contribution from ion-water interactions, both from localized surface charges and adsorbed ions, although the relative contribution of the former is larger on liposome surfaces. In this perspective, ion-water interaction energy values derived from experimental data for various ions are compared with theoretical values in the literature. Ultimately, quantifying ion-induced changes in the surface energy for the purpose of developing valid theoretical models for ion-water interactions will be critical to rationalizing the Hofmeister effect.

Project description:Escherichia coli adapts to changing environmental osmolality to survive and maintain growth. It has been shown that the diffusion of green fluorescent protein (GFP) in cells adapted to osmotic upshifts is higher than expected from the increase in biopolymer volume fraction. To better understand the physicochemical state of the cytoplasm in adapted cells, we now follow the macromolecular crowding during adaptation with fluorescence resonance energy transfer (FRET)-based sensors. We apply an osmotic upshift and find that after an initial increase, the apparent crowding decreases over the course of hours to arrive at a value lower than that before the osmotic upshift. Crowding relates to cell volume until cell division ensues, after which a transition in the biochemical organization occurs. Analysis of single cells by microfluidics shows that changes in cell volume, elongation, and division are most likely not the cause for the transition in organization. We further show that the decrease in apparent crowding upon adaptation is similar to the apparent crowding in energy-depleted cells. Based on our findings in combination with literature data, we suggest that adapted cells have indeed an altered biochemical organization of the cytoplasm, possibly due to different effective particle size distributions and concomitant nanoscale heterogeneity. This could potentially be a general response to accommodate higher biopolymer fractions yet retaining crowding homeostasis, and it could apply to other species or conditions as well.IMPORTANCE Bacteria adapt to ever-changing environmental conditions such as osmotic stress and energy limitation. It is not well understood how biomolecules reorganize themselves inside Escherichia coli under these conditions. An altered biochemical organization would affect macromolecular crowding, which could influence reaction rates and diffusion of macromolecules. In cells adapted to osmotic upshift, protein diffusion is indeed faster than expected on the basis of the biopolymer volume fraction. We now probe the effects of macromolecular crowding in cells adapted to osmotic stress or depleted in metabolic energy with a genetically encoded fluorescence-based probe. We find that the effective macromolecular crowding in adapted and energy-depleted cells is lower than in unstressed cells, indicating major alterations in the biochemical organization of the cytoplasm.

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Specific ion effects on macromolecular interactions in Escherichia coli extracts.

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Specific ion effects on macromolecular interactions in Escherichia coli extracts.

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