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Results: 1 to 20 of 105

1.

Unraveling the enigmatic mechanism of L-asparaginase II with QM/QM calculations.

Gesto DS, Cerqueira NM, Fernandes PA, Ramos MJ.

J Am Chem Soc. 2013 May 15;135(19):7146-58. doi: 10.1021/ja310165u. Epub 2013 May 6.

PMID:
23544711
[PubMed - indexed for MEDLINE]
2.

Mechanisms of antibiotic resistance: QM/MM modeling of the acylation reaction of a class A beta-lactamase with benzylpenicillin.

Hermann JC, Hensen C, Ridder L, Mulholland AJ, Höltje HD.

J Am Chem Soc. 2005 Mar 30;127(12):4454-65.

PMID:
15783228
[PubMed - indexed for MEDLINE]
3.

Investigation of the mechanism of the cell wall DD-carboxypeptidase reaction of penicillin-binding protein 5 of Escherichia coli by quantum mechanics/molecular mechanics calculations.

Shi Q, Meroueh SO, Fisher JF, Mobashery S.

J Am Chem Soc. 2008 Jul 23;130(29):9293-303. doi: 10.1021/ja801727k. Epub 2008 Jun 25.

PMID:
18576637
[PubMed - indexed for MEDLINE]
4.

Probing the role of threonine and serine residues of E. coli asparaginase II by site-specific mutagenesis.

Derst C, Henseling J, Röhm KH.

Protein Eng. 1992 Dec;5(8):785-9.

PMID:
1287659
[PubMed - indexed for MEDLINE]
5.

A covalently bound catalytic intermediate in Escherichia coli asparaginase: crystal structure of a Thr-89-Val mutant.

Palm GJ, Lubkowski J, Derst C, Schleper S, Röhm KH, Wlodawer A.

FEBS Lett. 1996 Jul 22;390(2):211-6.

PMID:
8706862
[PubMed - indexed for MEDLINE]
Free Article
6.

The mechanism of autocatalytic activation of plant-type L-asparaginases.

Michalska K, Hernandez-Santoyo A, Jaskolski M.

J Biol Chem. 2008 May 9;283(19):13388-97. doi: 10.1074/jbc.M800746200. Epub 2008 Mar 10.

PMID:
18334484
[PubMed - indexed for MEDLINE]
Free Article
7.

o-Quinone methide as alkylating agent of nitrogen, oxygen, and sulfur nucleophiles. The role of H-bonding and solvent effects on the reactivity through a DFT computational study.

Di Valentin C, Freccero M, Zanaletti R, Sarzi-Amadè M.

J Am Chem Soc. 2001 Aug 29;123(34):8366-77.

PMID:
11516286
[PubMed - indexed for MEDLINE]
8.

Determinants of regioselectivity and chemoselectivity in fosfomycin resistance protein FosA from QM/MM calculations.

Liao RZ, Thiel W.

J Phys Chem B. 2013 Feb 7;117(5):1326-36. doi: 10.1021/jp4002719. Epub 2013 Jan 28.

PMID:
23320732
[PubMed - indexed for MEDLINE]
9.

Mechanism of formation of the internal aldimine in pyridoxal 5'-phosphate-dependent enzymes.

Oliveira EF, Cerqueira NM, Fernandes PA, Ramos MJ.

J Am Chem Soc. 2011 Oct 5;133(39):15496-505. doi: 10.1021/ja204229m. Epub 2011 Sep 13.

PMID:
21854048
[PubMed - indexed for MEDLINE]
10.

Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.

Ranaghan KE, Ridder L, Szefczyk B, Sokalski WA, Hermann JC, Mulholland AJ.

Org Biomol Chem. 2004 Apr 7;2(7):968-80. Epub 2004 Mar 3.

PMID:
15034619
[PubMed - indexed for MEDLINE]
11.

ONIOM (DFT:MM) study of the catalytic mechanism of myo-inositol monophosphatase: essential role of water in enzyme catalysis in the two-metal mechanism.

Wang X, Hirao H.

J Phys Chem B. 2013 Jan 24;117(3):833-42. doi: 10.1021/jp312483n. Epub 2013 Jan 11.

PMID:
23268704
[PubMed - indexed for MEDLINE]
12.

Cloning, expression and characterisation of Erwinia carotovora L-asparaginase.

Kotzia GA, Labrou NE.

J Biotechnol. 2005 Oct 10;119(4):309-23.

PMID:
15951039
[PubMed - indexed for MEDLINE]
13.

High level QM/MM modeling of the formation of the tetrahedral intermediate in the acylation of wild type and K73A mutant TEM-1 class A beta-lactamase.

Hermann JC, Pradon J, Harvey JN, Mulholland AJ.

J Phys Chem A. 2009 Oct 29;113(43):11984-94. doi: 10.1021/jp9037254.

PMID:
19791786
[PubMed - indexed for MEDLINE]
14.

Elucidation of the specific function of the conserved threonine triad responsible for human L-asparaginase autocleavage and substrate hydrolysis.

Nomme J, Su Y, Lavie A.

J Mol Biol. 2014 Jun 26;426(13):2471-85. doi: 10.1016/j.jmb.2014.04.016. Epub 2014 Apr 22.

PMID:
24768817
[PubMed - indexed for MEDLINE]
15.

Thermochemical analysis and kinetics aspects for a chemical model for camphene ozonolysis.

Oliveira RC, Bauerfeldt GF.

J Chem Phys. 2012 Oct 7;137(13):134306. doi: 10.1063/1.4757150.

PMID:
23039598
[PubMed - indexed for MEDLINE]
16.

The catalytic mechanism of mouse renin studied with QM/MM calculations.

Brás NF, Ramos MJ, Fernandes PA.

Phys Chem Chem Phys. 2012 Sep 28;14(36):12605-13. doi: 10.1039/c2cp41422h. Epub 2012 Jul 13.

PMID:
22796659
[PubMed - indexed for MEDLINE]
17.

Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.

Zhou Y, Wang S, Zhang Y.

J Phys Chem B. 2010 Jul 8;114(26):8817-25. doi: 10.1021/jp104258d.

PMID:
20550161
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Active site cysteine is protonated in the PAD4 Michaelis complex: evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.

Ke Z, Zhou Y, Hu P, Wang S, Xie D, Zhang Y.

J Phys Chem B. 2009 Sep 24;113(38):12750-8. doi: 10.1021/jp903173c.

PMID:
19507815
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

MurD ligase from E. coli: Tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method.

Perdih A, Hodoscek M, Solmajer T.

Proteins. 2009 Feb 15;74(3):744-59. doi: 10.1002/prot.22188.

PMID:
18704940
[PubMed - indexed for MEDLINE]
20.

Atomistic details of the associative phosphodiester cleavage in human ribonuclease H.

Elsässer B, Fels G.

Phys Chem Chem Phys. 2010 Sep 28;12(36):11081-8. doi: 10.1039/c001097a. Epub 2010 Jul 30.

PMID:
20672157
[PubMed - indexed for MEDLINE]
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