Literature DB >> 21306147

Effect of osmolytes on protein dynamics in the lactate dehydrogenase-catalyzed reaction.

Nickolay Zhadin1, Robert Callender.   

Abstract

Laser-induced temperature jump relaxation spectroscopy was used to probe the effect of osmolytes on the microscopic rate constants of the lactate dehydrogenase-catalyzed reaction. NADH fluorescence and absorption relaxation kinetics were measured for the lactate dehydrogenase (LDH) reaction system in the presence of varying amounts of trimethylamine N-oxide (TMAO), a protein-stabilizing osmolyte, or urea, a protein-destabilizing osmolyte. Trimethylamine N-oxide (TMAO) at a concentration of 1 M strongly increases the rate of hydride transfer, nearly nullifies its activation energy, and also slightly increases the enthalpy of hydride transfer. In 1 M urea, the hydride transfer enthalpy is almost nullified, but the activation energy of the step is not affected significantly. TMAO increases the preference of the closed conformation of the active site loop in the LDH·NAD(+)·lactate complex; urea decreases it. The loop opening rate in the LDH·NADH·pyruvate complex changes its temperature dependence to inverse Arrhenius with TMAO. In this complex, urea accelerates the loop motion, without changing the loop opening enthalpy. A strong, non-Arrhenius decrease in the pyruvate binding rate in the presence of TMAO offers a decrease in the fraction of the open loop, pyruvate binding competent form at higher temperatures. The pyruvate off rate is not affected by urea but decreases with TMAO. Thus, the osmolytes strongly affect the rates and thermodynamics of specific events along the LDH-catalyzed reaction: binding of substrates, loop closure, and the chemical event. Qualitatively, these results can be understood as an osmolyte-induced change in the energy landscape of the protein complexes, shifting the conformational nature of functional substates within the protein ensemble.

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Year:  2011        PMID: 21306147      PMCID: PMC3075470          DOI: 10.1021/bi1018545

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  29 in total

1.  Dynamics of protein ligand binding on multiple time scales: NADH binding to lactate dehydrogenase.

Authors:  H Deng; N Zhadin; R Callender
Journal:  Biochemistry       Date:  2001-04-03       Impact factor: 3.162

Review 2.  Protein stabilization by naturally occurring osmolytes.

Authors:  D W Bolen
Journal:  Methods Mol Biol       Date:  2001

3.  Lactate dehydrogenase undergoes a substantial structural change to bind its substrate.

Authors:  Linlin Qiu; Miriam Gulotta; Robert Callender
Journal:  Biophys J       Date:  2007-05-04       Impact factor: 4.033

4.  Ligand binding and protein dynamics in lactate dehydrogenase.

Authors:  J R Exequiel T Pineda; Robert Callender; Steven D Schwartz
Journal:  Biophys J       Date:  2007-05-04       Impact factor: 4.033

5.  Incorporation of hydrostatic pressure into models of hydrogen tunneling highlights a role for pressure-modulated promoting vibrations.

Authors:  Sam Hay; Nigel S Scrutton
Journal:  Biochemistry       Date:  2008-08-22       Impact factor: 3.162

6.  On the pathway of forming enzymatically productive ligand-protein complexes in lactate dehydrogenase.

Authors:  Hua Deng; Scott Brewer; Dung M Vu; Keith Clinch; Robert Callender; R Brian Dyer
Journal:  Biophys J       Date:  2008-04-04       Impact factor: 4.033

7.  Toward an understanding of the role of dynamics on enzymatic catalysis in lactate dehydrogenase.

Authors:  Miriam Gulotta; Hua Deng; Hong Deng; R Brian Dyer; Robert H Callender
Journal:  Biochemistry       Date:  2002-03-12       Impact factor: 3.162

8.  Hydrogen exchange kinetics of RNase A and the urea:TMAO paradigm.

Authors:  Youxing Qu; D Wayne Bolen
Journal:  Biochemistry       Date:  2003-05-20       Impact factor: 3.162

9.  Probing the role of dynamics in hydride transfer catalyzed by lactate dehydrogenase.

Authors:  Nickolay Zhadin; Miriam Gulotta; Robert Callender
Journal:  Biophys J       Date:  2008-05-16       Impact factor: 4.033

10.  Trimethylamine oxide stabilizes teleost and mammalian lactate dehydrogenases against inactivation by hydrostatic pressure and trypsinolysis.

Authors:  P H Yancey; J F Siebenaller
Journal:  J Exp Biol       Date:  1999-12       Impact factor: 3.312

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  10 in total

1.  Resolution of Submillisecond Kinetics of Multiple Reaction Pathways for Lactate Dehydrogenase.

Authors:  Michael J Reddish; Robert Callender; R Brian Dyer
Journal:  Biophys J       Date:  2017-05-09       Impact factor: 4.033

2.  Thermodynamic and Structural Adaptation Differences between the Mesophilic and Psychrophilic Lactate Dehydrogenases.

Authors:  Sergei Khrapunov; Eric Chang; Robert H Callender
Journal:  Biochemistry       Date:  2017-07-05       Impact factor: 3.162

Review 3.  Redox, haem and CO in enzymatic catalysis and regulation.

Authors:  Stephen W Ragsdale; Li Yi; Güneş Bender; Nirupama Gupta; Yan Kung; Lifen Yan; Troy A Stich; Tzanko Doukov; Lars Leichert; Paul M Jenkins; Christopher M Bianchetti; Simon J George; Stephen P Cramer; R David Britt; Ursula Jakob; Jeffrey R Martens; George N Phillips; Catherine L Drennan
Journal:  Biochem Soc Trans       Date:  2012-06-01       Impact factor: 5.407

4.  In Vivo Titration of Folate Pathway Enzymes.

Authors:  Deepika Nambiar; Timkhite-Kulu Berhane; Robert Shew; Bryan Schwarz; Michael R Duff; Elizabeth E Howell
Journal:  Appl Environ Microbiol       Date:  2018-09-17       Impact factor: 4.792

5.  Large scale dynamics of the Michaelis complex in Bacillus stearothermophilus lactate dehydrogenase revealed by a single-tryptophan mutant study.

Authors:  Beining Nie; Hua Deng; Ruel Desamero; Robert Callender
Journal:  Biochemistry       Date:  2013-03-07       Impact factor: 3.162

6.  Active-Loop Dynamics within the Michaelis Complex of Lactate Dehydrogenase from Bacillus stearothermophilus.

Authors:  Beining Nie; Kara Lodewyks; Hua Deng; Ruel Z B Desamero; Robert Callender
Journal:  Biochemistry       Date:  2016-06-30       Impact factor: 3.162

7.  Mechanism of Thermal Adaptation in the Lactate Dehydrogenases.

Authors:  Huo-Lei Peng; Tsuyoshi Egawa; Eric Chang; Hua Deng; Robert Callender
Journal:  J Phys Chem B       Date:  2015-11-24       Impact factor: 2.991

8.  Direct evidence of catalytic heterogeneity in lactate dehydrogenase by temperature jump infrared spectroscopy.

Authors:  Michael J Reddish; Huo-Lei Peng; Hua Deng; Kunal S Panwar; Robert Callender; R Brian Dyer
Journal:  J Phys Chem B       Date:  2014-09-04       Impact factor: 2.991

9.  Pressure tolerance of deep-sea enzymes can be evolved through increasing volume changes in protein transitions: a study with lactate dehydrogenases from abyssal and hadal fishes.

Authors:  Mackenzie E Gerringer; Paul H Yancey; Olga V Tikhonova; Nikita E Vavilov; Victor G Zgoda; Dmitri R Davydov
Journal:  FEBS J       Date:  2020-04-21       Impact factor: 5.542

10.  Energy landscape of the Michaelis complex of lactate dehydrogenase: relationship to catalytic mechanism.

Authors:  Huo-Lei Peng; Hua Deng; R Brian Dyer; Robert Callender
Journal:  Biochemistry       Date:  2014-03-11       Impact factor: 3.162

  10 in total

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