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Items: 1 to 20 of 99

1.

Simulating the catalytic effect of a designed mononuclear zinc metalloenzyme that catalyzes the hydrolysis of phosphate triesters.

Singh MK, Chu ZT, Warshel A.

J Phys Chem B. 2014 Oct 23;118(42):12146-52. doi: 10.1021/jp507592g. Epub 2014 Oct 13.

2.

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase.

Frushicheva MP, Cao J, Chu ZT, Warshel A.

Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16869-74. doi: 10.1073/pnas.1010381107. Epub 2010 Sep 9.

3.

Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis.

Frushicheva MP, Cao J, Warshel A.

Biochemistry. 2011 May 10;50(18):3849-58. doi: 10.1021/bi200063a. Epub 2011 Apr 15.

4.

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.

Khare SD, Kipnis Y, Greisen P Jr, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL, Silman I, Leader H, Sussman JL, Stoddard BL, Tawfik DS, Baker D.

Nat Chem Biol. 2012 Feb 5;8(3):294-300. doi: 10.1038/nchembio.777.

5.

On the challenge of exploring the evolutionary trajectory from phosphotriesterase to arylesterase using computer simulations.

Bora RP, Mills MJ, Frushicheva MP, Warshel A.

J Phys Chem B. 2015 Feb 26;119(8):3434-45. doi: 10.1021/jp5124025. Epub 2015 Feb 13.

PMID:
25620270
7.

Computer aided enzyme design and catalytic concepts.

Frushicheva MP, Mills MJ, Schopf P, Singh MK, Prasad RB, Warshel A.

Curr Opin Chem Biol. 2014 Aug;21:56-62. doi: 10.1016/j.cbpa.2014.03.022. Epub 2014 May 8. Review.

8.

Theoretical aspects of hydrolysis of peptide bonds by zinc metalloenzymes.

Navrátil V, Klusák V, Rulíšek L.

Chemistry. 2013 Dec 2;19(49):16634-45. doi: 10.1002/chem.201302663. Epub 2013 Nov 5.

PMID:
24194391
9.

Challenges and advances in the computational modeling of biological phosphate hydrolysis.

Petrović D, Szeler K, Kamerlin SCL.

Chem Commun (Camb). 2018 Mar 28;54(25):3077-3089. doi: 10.1039/c7cc09504j. Epub 2018 Feb 7. Review.

PMID:
29412205
10.

Valence bond and enzyme catalysis: a time to break down and a time to build up.

Sharir-Ivry A, Varatharaj R, Shurki A.

Chemistry. 2015 May 4;21(19):7159-69. doi: 10.1002/chem.201406236. Epub 2015 Mar 24.

PMID:
25808731
11.

Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.

Ferrer S, Ruiz-Pernía J, Martí S, Moliner V, Tuñón I, Bertrán J, Andrés J.

Adv Protein Chem Struct Biol. 2011;85:81-142. doi: 10.1016/B978-0-12-386485-7.00003-X. Review.

PMID:
21920322
12.

Phosphate mono- and diesterase activities of the trinuclear zinc enzyme nuclease P1--insights from quantum chemical calculations.

Liao RZ, Yu JG, Himo F.

Inorg Chem. 2010 Aug 2;49(15):6883-8. doi: 10.1021/ic100266n.

PMID:
20604512
13.

Toward accurate screening in computer-aided enzyme design.

Roca M, Vardi-Kilshtain A, Warshel A.

Biochemistry. 2009 Apr 14;48(14):3046-56. doi: 10.1021/bi802191b.

14.

Catalytic zinc complexes for phosphate diester hydrolysis.

Tirel EY, Bellamy Z, Adams H, Lebrun V, Duarte F, Williams NH.

Angew Chem Int Ed Engl. 2014 Jul 28;53(31):8246-50. doi: 10.1002/anie.201400335. Epub 2014 Jun 11.

15.

Quantum mechanics/molecular mechanics investigation of the mechanism of phosphate transfer in human uridine-cytidine kinase 2.

Smith AJ, Li Y, Houk KN.

Org Biomol Chem. 2009 Jul 7;7(13):2716-24. doi: 10.1039/b901429b. Epub 2009 May 6.

16.

Computer simulations of enzyme catalysis: methods, progress, and insights.

Warshel A.

Annu Rev Biophys Biomol Struct. 2003;32:425-43. Epub 2003 Feb 5. Review.

PMID:
12574064
17.

Catalysis by a de novo zinc-mediated protein interface: implications for natural enzyme evolution and rational enzyme engineering.

Der BS, Edwards DR, Kuhlman B.

Biochemistry. 2012 May 8;51(18):3933-40. doi: 10.1021/bi201881p. Epub 2012 Apr 24.

18.

Phosphate monoester hydrolysis by trinuclear alkaline phosphatase; DFT study of transition States and reaction mechanism.

Chen SL, Liao RZ.

Chemphyschem. 2014 Aug 4;15(11):2321-30. doi: 10.1002/cphc.201402016. Epub 2014 Mar 28.

PMID:
24683174
19.
20.

Theoretical modeling of the reaction mechanism of phosphate monoester hydrolysis in alkaline phosphatase.

López-Canut V, Martí S, Bertrán J, Moliner V, Tuñón I.

J Phys Chem B. 2009 Jun 4;113(22):7816-24. doi: 10.1021/jp901444g.

PMID:
19425583

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