skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Hydrolysis of DFP and the Nerve Agent ( S )-Sarin by DFPase Proceeds along Two Different Reaction Pathways: Implications for Engineering Bioscavengers

Journal Article · · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
DOI:https://doi.org/10.1021/jp410422c· OSTI ID:1177836
 [1];  [2];  [3];  [1];  [4]
  1. UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States, Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
  2. Institut de Biologie Structurale “Jean-Pierre Ebel”, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
  3. Center for Structural and Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
  4. UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States

Sponsoring Organization:
USDOE National Nuclear Security Administration (NNSA)
Grant/Contract Number:
AC05-00OR22752
OSTI ID:
1177836
Journal Information:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry, Journal Name: Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry Vol. 118 Journal Issue: 17; ISSN 1520-6106
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 30 works
Citation information provided by
Web of Science

References (66)

Differences in amino acid residues in the binding pockets dictate substrate specificities of mouse senescence marker protein-30, human paraoxonase1, and squid diisopropylfluorophosphatase journal May 2012
The Histidine 115-Histidine 134 Dyad Mediates the Lactonase Activity of Mammalian Serum Paraoxonases journal March 2006
Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 Å resolution journal September 2003
Description of pentacoordinated phosphorus under an external electric field: which basis sets and semi-empirical methods are needed? journal January 2008
Enzymes for the Homeland Defense: Optimizing Phosphotriesterase for the Hydrolysis of Organophosphate Nerve Agents journal July 2012
Catalytic detoxification journal January 2011
The evolution of function in strictosidine synthase-like proteins: Strictosidine Synthase-Like Proteins journal September 2011
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme journal May 1976
Density-functional exchange-energy approximation with correct asymptotic behavior journal September 1988
Multidimensional free-energy calculations using the weighted histogram analysis method journal November 1995
Evolution of and perspectives on therapeutic approaches to nerve agent poisoning journal September 2011
IUPAC recommendations for the representation of reaction mechanisms journal October 1989
Reversed Enantioselectivity of Diisopropyl Fluorophosphatase against Organophosphorus Nerve Agents by Rational Design journal December 2009
Hydrolysis of Phosphotriesters: A Theoretical Analysis of the Enzymatic and Solution Mechanisms journal June 2012
Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis journal August 1980
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes journal March 1977
A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions journal July 2010
Crystal structures of oxime-bound fenamiphos-acetylcholinesterases: Reactivation involving flipping of the His447 ring to form a reactive Glu334–His447–oxime triad journal February 2010
Progress in the development of enzyme-based nerve agent bioscavengers journal December 2013
Senescence marker protein 30 functions as gluconolactonase in L-ascorbic acid biosynthesis, and its knockout mice are prone to scurvy journal April 2006
Enzymatic Mechanisms of Phosphate and Sulfate Transfer journal August 2006
Comparison of simple potential functions for simulating liquid water journal July 1983
The pDynamo Program for Molecular Simulations using Hybrid Quantum Chemical and Molecular Mechanical Potentials journal June 2008
Self‐consistent molecular orbital methods. XX. A basis set for correlated wave functions journal January 1980
Structure−Reactivity Studies of Serum Paraoxonase PON1 Suggest that Its Native Activity Is Lactonase journal April 2005
QM/MM Methods for Biomolecular Systems journal January 2009
Catalytic mechanisms for phosphotriesterases journal January 2013
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing journal November 2012
Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement journal January 2009
Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials
  • Eichkorn, Karin; Weigend, Florian; Treutler, Oliver
  • Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 97, Issue 1-4 https://doi.org/10.1007/s002140050244
journal October 1997
CHARMM: The biomolecular simulation program journal July 2009
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges journal November 2012
Exchange functionals with improved long-range behavior and adiabatic connection methods without adjustable parameters: The mPW and mPW1PW models journal January 1998
Empirical force fields for biological macromolecules: Overview and issues journal January 2004
Evolved Stereoselective Hydrolases for Broad-Spectrum G-Type Nerve Agent Detoxification journal April 2012
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu journal April 2010
Improved Treatment of the Protein Backbone in Empirical Force Fields journal January 2004
Effect of the damping function in dispersion corrected density functional theory journal March 2011
Density‐functional thermochemistry. III. The role of exact exchange journal April 1993
Stereochemistry and secondary reactions in the irreversible inhibition of serine hydrolases by organophosphorus compounds journal May 2004
Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations journal June 2011
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density journal January 1988
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems journal June 1993
In silico analyses of substrate interactions with human serum paraoxonase 1 journal May 2009
Kinetic analysis of interactions between human acetylcholinesterase, structurally different organophosphorus compounds and oximes journal December 2004
Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase journal January 2013
Density-functional approximation for the correlation energy of the inhomogeneous electron gas journal June 1986
Engineering V-Type Nerve Agents Detoxifying Enzymes Using Computationally Focused Libraries journal September 2013
Mechanisms and Free Energies of Enzymatic Reactions journal August 2006
Binding of a Designed Substrate Analogue to Diisopropyl Fluorophosphatase:  Implications for the Phosphotriesterase Mechanism journal October 2006
Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z=11–18 journal May 1980
Mutational and Structural Studies of the Diisopropylfluorophosphatase from Loligo vulgaris Shed New Light on the Catalytic Mechanism of the Enzyme journal June 2005
Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction journal July 2010
Insights into the reaction mechanism of the diisopropyl fluorophosphatase from Loligo vulgaris by means of kinetic studies, chemical modification and site-directed mutagenesis journal April 2001
Mechanistic insights into the hydrolysis of organophosphorus compounds by paraoxonase-1: exploring the limits of substrate tolerance in a promiscuous enzyme: SUBSTRATE TOLERANCE IN PARAOXONASE-1
  • Muthukrishnan, Sivaramakrishnan; Shete, Vivekanand S.; Sanan, Toby T.
  • Journal of Physical Organic Chemistry, Vol. 25, Issue 12 https://doi.org/10.1002/poc.3002
journal December 2012
Directed evolution of hydrolases for prevention of G-type nerve agent intoxication journal January 2011
Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris journal June 2001
Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements journal September 2007
First efficient uncharged reactivators for the dephosphylation of poisoned human acetylcholinesterase journal January 2011
Ageing and dealkylation of soman (pinacolylmethylphosphonofluoridate)-inactivated eel cholinesterase journal July 1967
Self-interaction correction to density-functional approximations for many-electron systems journal May 1981
Neutron structure and mechanistic studies of diisopropyl fluorophosphatase (DFPase) journal October 2010
Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields journal November 1994
Inductive and External Electric Field Effects in Pentacoordinated Phosphorus Compounds journal December 2007
Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes journal April 2004
VMD: Visual molecular dynamics journal February 1996