Probing volumetric properties of biomolecular systems by pressure perturbation calorimetry (PPC) – The effects of hydration, cosolvents and crowding

Suladze, Saba; Kahse, Marie; Erwin, Nelli; Tomazic, Daniel; Winter, Roland

doi:10.1016/j.ymeth.2014.08.007

Cited by 17 publications

(16 citation statements)

References 66 publications

(136 reference statements)

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“…Figure 1E shows that the increase in KCl concentration causes adrastic increase in the level of hydration of the folded 4U RNA, indicated by the more positive E8 8 values at 300 mm KCl. [14] This is in agreement with the finding that the ions remain hydrated upon association with the RNA. [13] Thethermally induced decrease of E8 8 for the folded RNAiscaused by partial dehydration of the RNAs urface and the vanishing difference between the water structure at the RNAs urface and the bulk.…”

supporting

confidence: 90%

“…[13] Thethermally induced decrease of E8 8 for the folded RNAiscaused by partial dehydration of the RNAs urface and the vanishing difference between the water structure at the RNAs urface and the bulk. [14] By integrating E8 8(T)over the transition region, we obtained the standard molar volume change of the heat-induced hairpinto-coil transition, DV o u T m ðÞ (Table S1). DV o u becomes more positive with increasing melting temperature,i ndicating ap ositive expansibility change, DE o u ,u pon unfolding.…”

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confidence: 99%

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Modulation of the Thermodynamic Signatures of an RNA Thermometer by Osmolytes and Salts

2017

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Folding of ribonucleic acids (RNAs) is driven by several factors, such as base pairing and stacking, chain entropy, and ion-mediated electrostatics, which have been studied in great detail. However, the power of background molecules in the cellular milieu is often neglected. Herein, we study the effect of common osmolytes on the folding equilibrium of a hairpin-structured RNA and, using pressure perturbation, provide novel thermodynamic and volumetric insights into the modulation mechanism. The presence of TMAO causes an increased thermal stability and a more positive volume change for the helix-to-coil transition, whereas urea destabilizes the hairpin and leads to an increased expansibility of the unfolded state. Further, we find a strong interplay between water, salt, and osmolyte in driving the thermodynamics and defining the temperature and pressure stability limit of the RNA. Our results support a universal working mechanism of TMAO and urea to (de)stabilize proteins and the RNA.

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confidence: 90%

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confidence: 99%

Modulation of the Thermodynamic Signatures of an RNA Thermometer by Osmolytes and Salts

2017

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“…Generally, Δ V u can be obtained from PPC measurements or spectroscopic approaches. In PPC, the coefficient of thermal expansion, α , of the partial volume of a biomolecule is deduced from the heat consumed or produced after small isothermal pressure‐jumps, thereby allowing the determination of α as a function of temperature, α ( T ), and the standard unfolding volume changes at the melting temperature,

Δ V_{u}^{normalo}

( T m,1bar ) . If the temperature‐dependence of

Δ V_{u}^{normalo}

is known, the temperature effect can be corrected by extrapolating the

Δ V_{u}^{normalo}

values to a reference temperature.…”

Section: Cosolvent Effects On the Folding Equilibrium Of Proteins Anmentioning

confidence: 99%

“…In PPC, the coefficient of thermal expansion, a,o ft he partial volumeo fabiomolecule is deduced from the heat consumed or produced after small isothermal pressure-jumps,t hereby allowing the determinationo fa as a functiono ft emperature, a(T), and the standard unfolding volumec hanges at the meltingt emperature, DV o u (T m,1bar ). [157] If the temperature-dependence of DV o u is known, the temperature effect can be corrected by extrapolatingt he DV o u values to ar eference temperature. As an example, we re-examined our previousP PC results for the cosolvent effect on the folding stabilityo fS Nase ( Figure 5).…”

Section: Pressure Perturbationmentioning

confidence: 99%

Crowders and Cosolvents—Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses

et al. 2017

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The free energy and conformational landscape of biomolecular systems as well as biochemical reactions depend not only on temperature and pressure, but also on the particular solution conditions. Such conditions include the effects of cosolvents (for example osmolytes) and macromolecular crowding, which are crucial components to understand the energetics and kinetics of biological processes in living system. Such conditions are also important for the understanding of many debilitating diseases, such as those where misfolding and amyloid formation of proteins are involved. Moreover, understanding their effects on biomolecular processes is prerequisite for designing industrially relevant enzymatic reactions, which seldom take place under neat conditions. Here, we review and discuss experimental and theoretical studies on the characterization of cosolvent and crowding induced effects in biologically relevant systems, approaching even the complexity of living organisms. In particular, we focus on cosolvent and crowding effects on the conformational equilibrium and folding kinetics of proteins and nucleic acids as well as on enzymatic reactions, including their effects on the temperature and pressure dependence of these processes. By presenting a few representative examples, we show how such effects are unveiled and described in thermodynamic and kinetic terms.

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“…There are relatively few studies on small molecules in water using PPC analysis [6–8]. The majority of published studies investigate macromolecules including synthetic polymers [5, 9–11], proteins [12–17] and nucleic acids [18, 19] in pure water or in buffered solutions. The results are expressed as the calculated thermal expansion coefficient ( α ).…”

Section: Introductionmentioning

confidence: 99%

Analysis of Mesoscopic Structured 2-Propanol/Water Mixtures Using Pressure Perturbation Calorimetry and Molecular Dynamic Simulation

et al. 2016

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In this paper we demonstrate the application of pressure perturbation calorimetry (PPC) to the characterization of 2-propanol/water mixtures. PPC of different 2-propanol/water mixtures provides two useful measurements: (i) the change in heat (ΔQ); and (ii) the value. The results demonstrate that the ΔQ values of the mixtures deviate from that expected for a random mixture, with a maximum at ~20–25 mol% 2-propanol. This coincides with the concentration at which molecular dynamics (MD) simulations show a maximum deviation from random distribution, and also the point at which alcohol–alcohol hydrogen bonds become dominant over alcohol–water hydrogen bonds. Furthermore, the value showed transitions at 2.5 mol% 2-propanol and at approximately 14 mol% 2-propanol. Below 2.5 mol% 2-propanol the values of are negative; this is indicative of the presence of isolated 2-propanol molecules surrounded by water molecules. Above 2.5 mol% 2-propanol rises, reaching a maximum at ~14 mol% corresponding to a point where mixed alcohol–water networks are thought to dominate. The values and trends identified by PPC show excellent agreement not only with those obtained from MD simulations but also with results in the literature derived using viscometry, THz spectroscopy, NMR and neutron diffraction.Electronic supplementary materialThe online version of this article (doi:10.1007/s10953-016-0554-y) contains supplementary material, which is available to authorized users.

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Probing volumetric properties of biomolecular systems by pressure perturbation calorimetry (PPC) – The effects of hydration, cosolvents and crowding

Cited by 17 publications

References 66 publications

Modulation of the Thermodynamic Signatures of an RNA Thermometer by Osmolytes and Salts

Modulation of the Thermodynamic Signatures of an RNA Thermometer by Osmolytes and Salts

Crowders and Cosolvents—Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses

Analysis of Mesoscopic Structured 2-Propanol/Water Mixtures Using Pressure Perturbation Calorimetry and Molecular Dynamic Simulation

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