Literature DB >> 12236744

Environmental effects on phosphoryl group bonding probed by vibrational spectroscopy: implications for understanding phosphoryl transfer and enzymatic catalysis.

Hu Cheng1, Ivana Nikolic-Hughes, Jianghua H Wang, Hua Deng, Patrick J O'Brien, Li Wu, Zhong-Yin Zhang, Daniel Herschlag, Robert Callender.   

Abstract

We have used vibrational spectroscopy to study bonding in monosubstituted dianionic phosphates, both to learn more about basic properties intrinsic to this important class of biological substrates and to assess the ability of vibrational spectroscopy to provide a "sensor" or probe of the local environment experienced by the phosphoryl group. We examined the bonding properties of the phosphoryl group via vibrational spectroscopy for a series of compounds in which the phosphoryl substituent was varied systematically and extensively. A broad linear correlation of the bridging P-O(R) bond length and the pK(a) of the substituent alcohol was observed. The results indicate that the P-O(R) bond changes by only approximately 0.04 A with alcohol substituents that vary in pK(a) by approximately 12 units, suggesting that phosphoryl group bonding responds in a subtle but regular manner to changes in the local environment. We also determined the effect on the phosphoryl bonding from changes in the solvent environment. Addition of dimethyl sulfoxide (DMSO) elongates the bridging bond, presumably as a result of lessened solvation to the nonbridging oxygens and conservation of bond order to phosphorus. Finally, we have addressed the relationship between ground-state bonding properties and reactivity, as changing the leaving group substituent and adding DMSO have large rate effects, and it was previously proposed that lengthening of the bond to be broken is the cause of the increased reactivity. The results herein suggest, however, that the change in the bridging bond energy is small compared to the changes in energy that accompany the observed reactivity differences. Further analysis indicates that electrostatic interactions can provide a common driving force underlying both bond lengthening and the observed rate increases. We suggest that ground-state distortions of substrates bound to enzymes can provide a readout of the electrostatic active site environment, an environment that is otherwise difficult to assess.

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Year:  2002        PMID: 12236744     DOI: 10.1021/ja026481z

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  13 in total

1.  Pyrophosphate activation in hypoxanthine--guanine phosphoribosyltransferase with transition state analogue.

Authors:  Hua Deng; Robert Callender; Vern L Schramm; Charles Grubmeyer
Journal:  Biochemistry       Date:  2010-03-30       Impact factor: 3.162

2.  Real-time structural transitions are coupled to chemical steps in ATP hydrolysis by Eg5 kinesin.

Authors:  Bokkyoo Jun; Sunyoung Kim
Journal:  J Biol Chem       Date:  2010-02-12       Impact factor: 5.157

Review 3.  Enzyme active site interactions by Raman/FTIR, NMR, and ab initio calculations.

Authors:  Hua Deng
Journal:  Adv Protein Chem Struct Biol       Date:  2013       Impact factor: 3.507

4.  Effect of Protein Isotope Labeling on the Catalytic Mechanism of Lactate Dehydrogenase.

Authors:  Tsuyoshi Egawa; Hua Deng; Eric Chang; Robert Callender
Journal:  J Phys Chem B       Date:  2019-11-06       Impact factor: 2.991

5.  Theoretical IR spectroscopy based on QM/MM calculations provides changes in charge distribution, bond lengths, and bond angles of the GTP ligand induced by the Ras-protein.

Authors:  Marco Klähn; Jürgen Schlitter; Klaus Gerwert
Journal:  Biophys J       Date:  2005-04-01       Impact factor: 4.033

6.  Thermodynamic origin of the increased rate of hydrolysis of phosphate and phosphorothioate esters in DMSO/water mixtures.

Authors:  Kerensa Sorensen-Stowell; Alvan C Hengge
Journal:  J Org Chem       Date:  2006-09-15       Impact factor: 4.354

7.  Site-specific solvation of the photoexcited protochlorophyllide a in methanol: formation of the hydrogen-bonded intermediate state induced by hydrogen-bond strengthening.

Authors:  Guang-Jiu Zhao; Ke-Li Han
Journal:  Biophys J       Date:  2007-09-07       Impact factor: 4.033

Review 8.  Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes.

Authors:  Daniel Herschlag; Aditya Natarajan
Journal:  Biochemistry       Date:  2013-03-14       Impact factor: 3.162

9.  On the mechanism of ATP hydrolysis in F1-ATPase.

Authors:  Markus Dittrich; Shigehiko Hayashi; Klaus Schulten
Journal:  Biophys J       Date:  2003-10       Impact factor: 4.033

10.  Hyperconjugation-mediated solvent effects in phosphoanhydride bonds.

Authors:  Jean C Summerton; Jeffrey D Evanseck; Michael S Chapman
Journal:  J Phys Chem A       Date:  2012-10-09       Impact factor: 2.781

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