Trimethylamine-N-Oxide Counteracts Urea Effects on Rabbit Muscle Lactate Dehydrogenase Function: A Test of the Counteraction Hypothesis

Baskakov, Ilia V.; Wang, Ai‐Jun; Bolen, D. Wayne

doi:10.1016/s0006-3495(98)77972-x

Cited by 138 publications

(97 citation statements)

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“…Nevertheless, the calculated and experimental glycine backbone transfer free energies demonstrate reasonable agreement and account for the features of the protein folding ability of TMAO. 15,47,48 We obtained DG tr from the simulated solvation free energy differences between 2M osmolytes and pure water. These calculated transfer free energies of the peptide backbone demonstrated additivity of each incremental unit of the peptide backbone corresponding to a nearly constant change in the free energy for these short oligomers.…”

Section: Discussionmentioning

confidence: 99%

Backbone additivity in the transfer model of protein solvation

et al. 2010

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The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (DG tr ) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and DG tr values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of 254 cal/mol/M compares quite favorably with 243 cal/mol/M determined experimentally.

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Section: Discussionmentioning

confidence: 99%

Backbone additivity in the transfer model of protein solvation

et al. 2010

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“…Numerous studies have demonstrated that protecting osmolytes, such as trimethylamine N-oxide (TMAO), can force thermodynamically unstable proteins to fold 2 and stabilize folded proteins to withstand harsh conditions such as high temperature and denaturant concentrations. This favorable folding property of TMAO operates in an additive and independent manner with urea, [3][4][5] allowing counteraction of urea's destabilizing effects on protein stability in urea-rich cells. 6 Indeed, urea and TMAO are often found in a 2:1 molar ratio in marine cartilaginous fish, which in vitro has been shown to result in minimally changed stability.…”

Section: Introductionmentioning

confidence: 99%

Osmolyte‐induced conformational changes in the Hsp90 molecular chaperone

et al. 2009

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Osmolytes are small molecules that play a central role in cellular homeostasis and the stress response by maintaining protein thermodynamic stability at controlled levels. The underlying physical chemistry that describes how different osmolytes impact folding free energy is well understood, however little is known about their influence on other crucial aspects of protein behavior, such as native-state conformational changes. Here we investigate this issue with the Hsp90 molecular chaperone, a large dimeric protein that populates a complex conformational equilibrium. Using small angle X-ray scattering we observe dramatic osmolyte-dependent structural changes within the native ensemble. The degree to which different osmolytes affect the Hsp90 conformation strongly correlates with thermodynamic metrics of their influence on stability. This observation suggests that the well-established osmolyte principles that govern stability also apply to large-scale conformational changes, a proposition that is corroborated by structure-based fitting of the scattering data, surface area comparisons and m-value analysis. This approach shows how osmolytes affect a highly cooperative open/closed structural transition between two conformations that differ by a domain-domain interaction. Hsp90 adopts an additional ligandspecific conformation in the presence of ATP and we find that osmolytes do not significantly affect this conformational change. Together, these results extend the scope of osmolytes by suggesting that they can maintain protein conformational heterogeneity at controlled levels using similar underlying principles that allow them to maintain protein stability; however the relative impact of osmolytes on different structural states can vary significantly.

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“…TMAO can restore enzyme function that has been lost because of the presence of urea (6,(10)(11)(12) by restoring the protein to its native structure (13)(14)(15). The mechanism of action of these protective osmolytes is not understood fully; both direct (16)(17)(18)(19) and indirect (13,(19)(20)(21) interactions have been proposed, and the mechanism may be molecule-specific (14).…”

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confidence: 99%

Counteraction of urea-induced protein denaturation by trimethylamine N -oxide: A chemical chaperone at atomic resolution

Bennion

Daggett

2004

Proc. Natl. Acad. Sci. U.S.A.

300

287

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Proteins are very sensitive to their solvent environments. Urea is a common chemical denaturant of proteins, yet some animals contain high concentrations of urea. These animals have evolved an interesting mechanism to counteract the effects of urea by using trimethylamine N-oxide (TMAO). The molecular basis for the ability of TMAO to act as a chemical chaperone remains unknown. Here, we describe molecular dynamics simulations of a small globular protein, chymotrypsin inhibitor 2, in 8 M urea and 4 M TMAO͞8 M urea solutions, in addition to other control simulations, to investigate this effect at the atomic level. In 8 M urea, the protein unfolds, and urea acts in both a direct and indirect manner to achieve this effect. In contrast, introduction of 4 M TMAO counteracts the effect of urea and the protein remains well structured. TMAO makes few direct interactions with the protein. Instead, it prevents unfolding of the protein by structuring the solvent. In particular, TMAO orders the solvent and discourages it from competing with intraprotein H bonds and breaking up the hydrophobic core of the protein.M echanisms have evolved in nature to allow living organisms to compensate for extreme conditions. For example, certain marine creatures have adapted to life at high pressures and salinity by using osmolytes to maintain cellular volume and buoyancy (1, 2). However, certain osmolytes, like urea, can degrade protein function and disrupt their structures at the high concentrations found in some animals and marine life (1-3), although elevated pressures (Ϸ70 MPa) could mitigate some of the deleterious effects of urea (4-6). Nevertheless, the answer to this paradox was the discovery of protective osmolytes such as betaine and trimethylamine N-oxide (TMAO) in certain elasmobranchs by Yancey et al. (1,[7][8] and later in other marine organisms and mammals (1,6,9). In marine animals, the TMAO concentration varies with habitat depth, presumably as a response to pressure (4-5). Furthermore, in organisms that concentrate urea as an osmolyte (7) and buoyancy factor (2), TMAO has been found in urea at ratios of 3:1 and 2:1 (7, 10).TMAO can restore enzyme function that has been lost because of the presence of urea (6, 10-12) by restoring the protein to its native structure (13-15). The mechanism of action of these protective osmolytes is not understood fully; both direct (16)(17)(18)(19) and indirect (13,(19)(20)(21) interactions have been proposed, and the mechanism may be molecule-specific (14). Our understanding of the mechanism of action of chemical denaturants, such as urea and guanidinium chloride, is in a similar state (19,20,(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33). Consequently, we are pursuing molecular dynamics (MD) simulations of such compounds in an attempt to characterize these mechanisms at the molecular level.Here, we investigate the ability of TMAO to overcome the effect of urea on protein structure at the atomic level. Chymotrypsin inhibitor 2 (CI2) was chosen for this study because of the extensive amoun...

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Trimethylamine-N-Oxide Counteracts Urea Effects on Rabbit Muscle Lactate Dehydrogenase Function: A Test of the Counteraction Hypothesis

Cited by 138 publications

References 50 publications

Backbone additivity in the transfer model of protein solvation

Backbone additivity in the transfer model of protein solvation

Osmolyte‐induced conformational changes in the Hsp90 molecular chaperone

Counteraction of urea-induced protein denaturation by trimethylamine N -oxide: A chemical chaperone at atomic resolution

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