Literature DB >> 30638025

Dynamical Effects of Trimethylamine N-Oxide on Aqueous Solutions of Urea.

Xiaojing Teng1, Toshiko Ichiye1.   

Abstract

Trimethylamine N-oxide (TMAO) stabilizes protein structures, whereas urea destabilizes proteins, and their opposing effects can be counteracted at a 1:2 ratio of TMAO to urea. To investigate how they affect solution dynamics, molecular dynamics simulations have been carried out for aqueous solutions of TMAO and urea at different concentrations. In the binary solutions, urea mainly slows the diffusion of waters that are hydrogen bonded to it (i.e., hydration water), whereas TMAO dramatically slows the diffusion of both hydration water and bulk water because of long-lived TMAO-water hydrogen bonds. In the ternary solutions, because TMAO decreases the diffusion rate of bulk water, the lifetimes of not only water-water but also urea-water hydrogen bonds increase. In addition, the constant forming and breaking of short lifetime hydrogen bonds between urea and water appears to impart energy into the bulk, whereas the long lifetime hydrogen bonds between TMAO and water slows down the bulk, resulting in the compensating effects on bulk water in the ternary solution. This suggests that the counteracting effects of TMAO on urea denaturation may be both to make longer lived hydrogen bonds to water and to counter the energizing effects of urea on bulk water.

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Year:  2019        PMID: 30638025      PMCID: PMC7085122          DOI: 10.1021/acs.jpcb.8b09874

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  40 in total

1.  Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.

Authors:  Hans W Horn; William C Swope; Jed W Pitera; Jeffry D Madura; Thomas J Dick; Greg L Hura; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2004-05-22       Impact factor: 3.488

2.  Molecular mechanism for the preferential exclusion of TMAO from protein surfaces.

Authors:  Deepak R Canchi; Pruthvi Jayasimha; Donald C Rau; George I Makhatadze; Angel E Garcia
Journal:  J Phys Chem B       Date:  2012-10-01       Impact factor: 2.991

3.  The role of water coordination in binary mixtures. A study of two model amphiphilic molecules in aqueous solutions by molecular dynamics and NMR.

Authors:  R Sinibaldi; C Casieri; S Melchionna; G Onori; A L Segre; S Viel; L Mannina; F De Luca
Journal:  J Phys Chem B       Date:  2006-05-04       Impact factor: 2.991

4.  Volumetrically Derived Thermodynamic Profile of Interactions of Urea with a Native Protein.

Authors:  Ikbae Son; Tigran V Chalikian
Journal:  Biochemistry       Date:  2016-11-15       Impact factor: 3.162

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

Authors:  Brian J Bennion; Valerie Daggett
Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-19       Impact factor: 11.205

6.  Marine fish may be biochemically constrained from inhabiting the deepest ocean depths.

Authors:  Paul H Yancey; Mackenzie E Gerringer; Jeffrey C Drazen; Ashley A Rowden; Alan Jamieson
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-03       Impact factor: 11.205

7.  Why do some organisms use a urea-methylamine mixture as osmolyte? Thermodynamic compensation of urea and trimethylamine N-oxide interactions with protein.

Authors:  T Y Lin; S N Timasheff
Journal:  Biochemistry       Date:  1994-10-25       Impact factor: 3.162

8.  All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Authors:  A D MacKerell; D Bashford; M Bellott; R L Dunbrack; J D Evanseck; M J Field; S Fischer; J Gao; H Guo; S Ha; D Joseph-McCarthy; L Kuchnir; K Kuczera; F T Lau; C Mattos; S Michnick; T Ngo; D T Nguyen; B Prodhom; W E Reiher; B Roux; M Schlenkrich; J C Smith; R Stote; J Straub; M Watanabe; J Wiórkiewicz-Kuczera; D Yin; M Karplus
Journal:  J Phys Chem B       Date:  1998-04-30       Impact factor: 2.991

9.  Volume exclusion and H-bonding dominate the thermodynamics and solvation of trimethylamine-N-oxide in aqueous urea.

Authors:  Jörg Rösgen; Ruby Jackson-Atogi
Journal:  J Am Chem Soc       Date:  2012-02-10       Impact factor: 15.419

10.  Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters.

Authors:  In Suk Joung; Thomas E Cheatham
Journal:  J Phys Chem B       Date:  2009-10-08       Impact factor: 2.991

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  2 in total

1.  Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile.

Authors:  Qi Huang; Jocelyn M Rodgers; Russell J Hemley; Toshiko Ichiye
Journal:  Int J Mol Sci       Date:  2019-03-22       Impact factor: 5.923

2.  Dynamical Model for the Counteracting Effects of Trimethylamine N-Oxide on Urea in Aqueous Solutions under Pressure.

Authors:  Xiaojing Teng; Toshiko Ichiye
Journal:  J Phys Chem B       Date:  2020-02-27       Impact factor: 2.991

  2 in total

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