scholarly journals A Computational Study of the Hydrolysis of dGTP Analogues with Halomethylene-Modified Leaving Groups in Solution: Implications for the Mechanism of DNA Polymerases

Biochemistry ◽  
2009 ◽  
Vol 48 (25) ◽  
pp. 5963-5971 ◽  
Author(s):  
Shina C. L. Kamerlin ◽  
Charles E. McKenna ◽  
Myron F. Goodman ◽  
A. Warshel
Keyword(s):  
Computational Study ◽  
Dna Polymerases ◽  
Leaving Groups ◽  
Hydrolysis Of

A phenoxo-bridged dicopper(ii) complex as a model for phosphatase activity: mechanistic insights from a combined experimental and computational study

2017 ◽  
Vol 46 (12) ◽  
pp. 4038-4054 ◽  
Author(s):  
Suman K. Barman ◽  
Totan Mondal ◽  
Debasis Koley ◽  
Francesc Lloret ◽  
Rabindranath Mukherjee
Keyword(s):  
Dft Calculations ◽  
Phosphatase Activity ◽  
Theoretical Approach ◽  
Computational Study ◽  
Hydrolysis Of

Hydrolysis of RNA-model substrate HPNP by a dicopper(ii) complex has been studied with combined experimental and theoretical approach. Involvement of H-bonding has been probed by DFT calculations.

ChemInform Abstract: FAST HYDROLYSIS OF ALKYL RADICALS WITH LEAVING GROUPS IN THE β POSITION

1983 ◽  
Vol 14 (12) ◽  
Author(s):  
G. KOLTZENBURG ◽  
G. BEHRENS ◽  
D. SCHULTE-FROHLINDE
Keyword(s):  
Alkyl Radicals ◽  
Leaving Groups ◽  
Hydrolysis Of

scholarly journals Hydrolysis of nerve agents by model nucleophiles: A computational study

2008 ◽  
Vol 175 (1-3) ◽  
pp. 200-203 ◽  
Author(s):  
Jeremy M. Beck ◽  
Christopher M. Hadad
Keyword(s):  
Computational Study ◽  
Nerve Agents ◽  
Hydrolysis Of

Base Mechanism to the Hydrolysis of Phosphate Triester Promoted by the Cd2+/Cd2+ Active site of Phosphotriesterase: A Computational Study

2018 ◽  
Vol 57 (10) ◽  
pp. 5888-5902 ◽  
Author(s):  
Marcelo A. Chagas ◽  
Eufrásia S. Pereira ◽  
Marina P. B. Godinho ◽  
Júlio Cosme S. Da Silva ◽  
Willian R. Rocha
Keyword(s):  
Active Site ◽  
Computational Study ◽  
Base Mechanism ◽  
Hydrolysis Of

Studies in Solvolysis. Part VII. The Neutral Hydrolysis of Methyl Perchlorate

1975 ◽  
Vol 53 (20) ◽  
pp. 3106-3115 ◽  
Author(s):  
Ross Elmore Robertson ◽  
Adrianna Annesa ◽  
John Marshall William Scott
Keyword(s):  
Heat Capacity ◽  
Carbon Atom ◽  
Temperature Dependence ◽  
Thermodynamic Parameters ◽  
Isotope Effect ◽  
Perchlorate Ion ◽  
Rate Of Hydrolysis ◽  
Leaving Groups ◽  
Hydrolysis Of

The temperature dependence of the rate of hydrolysis of methyl perchlorate has been measured and the entropy (ΔS≠), enthalpy (ΔH≠), and heat capacity (ΔCp≠) of activation calculated. The measurements confirm that the perchlorate ion is superior to all other leaving groups in water. The isotope effect related to the hydrolysis of methyl-d3 perchlorate has been measured at three temperatures and shown to be inverse. The thermodynamic parameters and the isotope effect were examined with respect to the mechanism of substitution at a primary carbon atom.

Activating Water: Important Effects of Non-leaving Groups on the Hydrolysis of Phosphate Triesters

2011 ◽  
Vol 17 (52) ◽  
pp. 14996-15004 ◽  
Author(s):  
Anthony J. Kirby ◽  
Michelle Medeiros ◽  
Pedro S. M. Oliveira ◽  
Elisa S. Orth ◽  
Tiago A. S. Brandão ◽  
...  
Keyword(s):  
Leaving Groups ◽  
Hydrolysis Of

scholarly journals Comparative Biochemical and Computational Study of the Role of Naturally Occurring Mutations at Ambler Positions 104 and 170 in GES β-Lactamases

2010 ◽  
Vol 54 (11) ◽  
pp. 4864-4871 ◽  
Author(s):  
Stathis D. Kotsakis ◽  
Vivi Miriagou ◽  
Eva Tzelepi ◽  
Leonidas S. Tzouvelekis
Keyword(s):  
Boronic Acid ◽  
Computational Study ◽  
Dynamic Simulations ◽  
Site Specific ◽  
Catalytic Behavior ◽  
Naturally Occurring ◽  
Hydrolysis Rates ◽  
Hydrolysis Of ◽  
Precise Role

ABSTRACT In GES-type β-lactamases, positions 104 and 170 are occupied by Glu or Lys and by Gly, Asn, or Ser, respectively. Previous studies have indicated an important role of these amino acids in the interaction with β-lactams, although their precise role, especially that of residue 104, remains uncertain. In this study, we constructed GES-1 (Glu104, Gly170), GES-2 (Glu104, Asn170), GES-5 (Glu104, Ser170), GES-6 (Lys104, Ser170), GES-7 (Lys104, Gly170), and GES-13 (Lys104, Asn170) by site-specific mutagenesis and compared their hydrolytic properties. Isogenic comparisons of β-lactam resistance levels conferred by these GES variants were also performed. Data indicated the following patterns: (i) Lys104-containing enzymes exhibited enhanced hydrolysis of oxyimino-cephalosporins and reduced efficiency against imipenem in relation to enzymes possessing Glu104, (ii) Asn170-containing enzymes showed reduced hydrolysis rates of penicillins and older cephalosporins, (iii) Ser170 enabled GES to hydrolyze cefoxitin efficiently, and (iv) Asn170 and Ser170 increased the carbapenemase character of GES enzymes but reduced their activity against ceftazidime. Molecular dynamic simulations of GES apoenzyme models, as well as construction of GES structures complexed with cefoxitin and an achiral ceftazidime-like boronic acid, provided insights into the catalytic behavior of the studied mutants. There were indications that an increased stability of the hydrogen bonding network of Glu166-Lys73-Ser70 and an altered positioning of Trp105 correlated with the substrate spectra, especially with acylation of GES by imipenem. Furthermore, likely effects of Ser170 on GES interactions with cefoxitin and of Lys104 on interactions with oxyimino-cephalosporins were revealed. Overall, the data unveiled the importance of residues 104 and 170 in the function of GES enzymes.

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