Wong L

General

Full name : Wong Lilly

First name : Lilly

Mail : Dept. of Pharmacology, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0636

Zip Code :

City :

Country : USA

Email : lilly@phrtaylO.ucsd.edu

Phone : 619-534-0920

Fax :

Website :

Directory :

References (9)

Title : Detection and classification of organophosphate nerve agent simulants using support vector machines with multiarray sensors - Sadik_2004_J.Chem.Inf.Comput.Sci_44_499
Author(s) : Sadik O , Land WH, Jr. , Wanekaya AK , Uematsu M , Embrechts MJ , Wong L , Leibensperger D , Volykin A
Ref : J Chem Inf Comput Sci , 44 :499 , 2004
Abstract : The need for rapid and accurate detection systems is expanding and the utilization of cross-reactive sensor arrays to detect chemical warfare agents in conjunction with novel computational techniques may prove to be a potential solution to this challenge. We have investigated the detection, prediction, and classification of various organophosphate (OP) nerve agent simulants using sensor arrays with a novel learning scheme known as support vector machines (SVMs). The OPs tested include parathion, malathion, dichlorvos, trichlorfon, paraoxon, and diazinon. A new data reduction software program was written in MATLAB V. 6.1 to extract steady-state and kinetic data from the sensor arrays. The program also creates training sets by mixing and randomly sorting any combination of data categories into both positive and negative cases. The resulting signals were fed into SVM software for "pairwise" and "one" vs all classification. Experimental results for this new paradigm show a significant increase in classification accuracy when compared to artificial neural networks (ANNs). Three kernels, the S2000, the polynomial, and the Gaussian radial basis function (RBF), were tested and compared to the ANN. The following measures of performance were considered in the pairwise classification: receiver operating curve (ROC) Az indices, specificities, and positive predictive values (PPVs). The ROC Az) values, specifities, and PPVs increases ranged from 5% to 25%, 108% to 204%, and 13% to 54%, respectively, in all OP pairs studied when compared to the ANN baseline. Dichlorvos, trichlorfon, and paraoxon were perfectly predicted. Positive prediction for malathion was 95%.
ESTHER : Sadik_2004_J.Chem.Inf.Comput.Sci_44_499
PubMedSearch : Sadik_2004_J.Chem.Inf.Comput.Sci_44_499
PubMedID: 15032529

Title : Nanosecond dynamics of acetylcholinesterase near the active center gorge - Boyd_2004_J.Biol.Chem_279_26612
Author(s) : Boyd AE , Dunlop CS , Wong L , Radic Z , Taylor P , Johnson DA
Ref : Journal of Biological Chemistry , 279 :26612 , 2004
Abstract : To delineate the role of peptide backbone flexibility and rapid molecular motion in acetylcholinesterase catalysis and inhibitor association, we investigated the decay of fluorescence anisotropy at three sites of fluorescein conjugation to cysteine-substitution mutants of the enzyme. One cysteine was placed in a loop at the peripheral site near the rim of the active center gorge (H287C); a second was in a helical region outside of the active center gorge (T249C); a third was at the tip of a small, flexible omega loop well separated from the gorge (A262C). Mutation and fluorophore conjugation did not appreciably alter catalytic or inhibitor binding parameters of the enzyme. The results show that each site examined was associated with a high degree of segmental motion; however, the A262C and H287C sites were significantly more flexible than the T249C site. Association of the active center inhibitor, tacrine, and the peripheral site peptide inhibitor, fasciculin, had no effect on the anisotropy decay of fluorophores at positions 249 and 262. Fasciculin, but not tacrine, on the other hand, dramatically altered the decay profile of the fluorophore at the 287 position, in a manner consistent with fasciculin reducing the segmental motion of the peptide chain in this local region. The results suggest that the motions of residues near the active center gorge and across from the Cys(69)-Cys(96) omega loop are uncoupled and that ligand binding at the active center or the peripheral site does not influence acetylcholinesterase conformational dynamics globally, but induces primarily domain localized decreases in flexibility proximal to the bound ligand.
ESTHER : Boyd_2004_J.Biol.Chem_279_26612
PubMedSearch : Boyd_2004_J.Biol.Chem_279_26612
PubMedID: 15078872

Title : Poster (89) Phosphorylation of mouse cholinesterases and mutants by ddvp and reactivation of conjugates by Hi-6 and 2-PAM -
Author(s) : Kovarik Z , Wong L , Radic Z , Taylor P
Ref : In: Cholinesterases in the Second Millennium: Biomolecular and Pathological Aspects , (Inestrosa NC, Campos EO) P. Universidad Catolica de Chile-FONDAP Biomedicina :367 , 2004
PubMedID:

Title : Phosphorylation of mouse cholinesterases and mutants by DDVP and reactivation of conjugates by HI-6 and 2-PAM -
Author(s) : Kovarik Z , Wong L , Radic Z , Taylor P
Ref : In: Cholinesterases in the Second Millennium: Biomolecular and Pathological Aspects , (Inestrosa NC, Campos EO) P. Universidad Catolica de Chile-FONDAP Biomedicina :219 , 2004
PubMedID:

Title : Probing the active center Gorge of acetylcholinesterase by fluorophores Linked to substituted cysteines - Boyd_2000_J.Biol.Chem_275_22401
Author(s) : Boyd AE , Marnett AB , Wong L , Taylor P
Ref : Journal of Biological Chemistry , 275 :22401 , 2000
Abstract : To examine the influence of individual side chains in governing rates of ligand entry into the active center gorge of acetylcholinesterase and to characterize the dynamics and immediate environment of these residues, we have conjugated reactive groups with selected charge and fluorescence characteristics to cysteines substituted by mutagenesis at specific positions on the enzyme. Insertion of side chains larger than in the native tyrosine at position 124 near the constriction point of the active site gorge confers steric hindrance to affect maximum catalytic throughput (k(cat)/K(m)) and rates of diffusional entry of trifluoroketones to the active center. Smaller groups appear not to present steric constraints to entry; however, cationic side chains selectively and markedly reduce cation ligand entry through electrostatic repulsion in the gorge. The influence of side chain modification on ligand kinetics has been correlated with spectroscopic characteristics of fluorescent side chains and their capacity to influence the binding of a peptide, fasciculin, which inhibits catalysis peripherally by sealing the mouth of the gorge. Acrylodan conjugated to cysteine was substituted for tyrosine at position 124 within the gorge, for histidine 287 on the surface adjacent to the gorge and for alanine 262 on a mobile loop distal to the gorge. The 124 position reveals the most hydrophobic environment and the largest hypsochromic shift of the emission maximum with fasciculin binding. This finding likely reflects a sandwiching of the acrylodan in the complex with the tip of fasciculin loop II. An intermediate spectral shift is found for the 287 position, consistent with partial occlusion by loops II and III of fasciculin in the complex. Spectroscopic properties of the acrylodan at the 262 position are unaltered by fasciculin addition. Hence, combined spectroscopic and kinetic analyses reveal distinguishing characteristics in various regions of acetylcholinesterase that influence ligand association.
ESTHER : Boyd_2000_J.Biol.Chem_275_22401
PubMedSearch : Boyd_2000_J.Biol.Chem_275_22401
PubMedID: 10779503

Title : Mechanism of oxime reactivation of acetylcholinesterase analyzed by chirality and mutagenesis - Wong_2000_Biochemistry_39_5750
Author(s) : Wong L , Radic Z , Bruggemann RJ , Hosea NA , Berman HA , Taylor P
Ref : Biochemistry , 39 :5750 , 2000
Abstract : Organophosphates inactivate acetylcholinesterase by reacting covalently with the active center serine. We have examined the reactivation of a series of resolved enantiomeric methylphosphonate conjugates of acetylcholinesterase by two oximes, 2-pralidoxime (2-PAM) and 1-(2'-hydroxyiminomethyl-1'-pyridinium)-3-(4'-carbamoyl-1-pyridinium) (HI-6). The S(p) enantiomers of the methylphosphonate esters are far more reactive in forming the conjugate with the enzyme, and we find that rates of oxime reactivation also show an S(p) versus R(p) preference, suggesting that a similar orientation of the phosphonyl oxygen toward the oxyanion hole is required for both efficient inactivation and reactivation. A comparison of reactivation rates of (S(p))- and (R(p))-cycloheptyl, 3,3-dimethylbutyl, and isopropyl methylphosphonyl conjugates shows that steric hindrance by the alkoxy group precludes facile access of the oxime to the tetrahedral phosphorus. To facilitate access, we substituted smaller side chains in the acyl pocket of the active center and find that the Phe295Leu substitution enhances the HI-6-elicited reactivation rates of the S(p) conjugates up to 14-fold, whereas the Phe297Ile substitution preferentially enhances 2-PAM reactivation by as much as 125-fold. The fractional enhancement of reactivation achieved by these mutations of the acyl pocket is greatest for the conjugated phosphonates of the largest steric bulk. By contrast, little enhancement of the reactivation rate is seen with these mutants for the R(p) conjugates, where limitations on oxime access to the phosphonate and suboptimal positioning of the phosphonyl oxygen in the oxyanion hole may both slow reactivation. These findings suggest that impaction of the conjugated organophosphate within the constraints of the active center gorge is a major factor in influencing oxime access and reactivation rates. Moreover, the individual oximes differ in attacking orientation, leading to the presumed pentavalent transition state. Hence, their efficacies as reactivating agents depend on the steric bulk of the intervening groups surrounding the tetrahedral phosphorus.
ESTHER : Wong_2000_Biochemistry_39_5750
PubMedSearch : Wong_2000_Biochemistry_39_5750
PubMedID: 10801325

Title : Analysis of cholinesterase inactivation and reactivation by systematic structural modification and enantiomeric selectivity - Taylor_1999_Chem.Biol.Interact_119-120_3
Author(s) : Taylor P , Wong L , Radic Z , Tsigelny I , Bruggemann R , Hosea NA , Berman HA
Ref : Chemico-Biological Interactions , 119-120 :3 , 1999
Abstract : We show here with a congeneric series of Rp- and Sp-alkoxymethyl phosphonothiolates of known absolute stereochemistry that chiral selectivity in their reaction with acetylcholinesterase can be described in terms of discrete orientational and steric requirements. Stereoselectivity depends on acyl pocket dimensions, which govern leaving group orientation and a productive association of the phosphonyl oxygen in the oxyanion hole. Overall geometry is consistent with a pentavalent intermediate where the attacking serine and leaving group are at apical positions. Oxime reactivation of the phosphonylated enzyme occurs through a similar associative intermediate presumably forming an oxime phosphonate. The oximes of differing structure show distinct angles of attacking the phosphate where the attack angles and access to the phosphorus are constrained in the sterically impacted gorge. Hence, efficacy of oxime reactivation is dependent on both oxime and conjugated phosphonate structures.
ESTHER : Taylor_1999_Chem.Biol.Interact_119-120_3
PubMedSearch : Taylor_1999_Chem.Biol.Interact_119-120_3
PubMedID: 10421434

Title : Acetylcholinesterase Structural Perturbations Examined Through Cysteine Substitution Mutagenesis -
Author(s) : Boyd AE , Wong L , Taylor P
Ref : In: Structure and Function of Cholinesterases and Related Proteins - Proceedings of Sixth International Meeting on Cholinesterases , (Doctor, B.P., Taylor, P., Quinn, D.M., Rotundo, R.L., Gentry, M.K. Eds) Plenum Publishing Corp. :452 , 1998
PubMedID:

Title : Reactivation of Enantiomeric Organophosphonyl Conjugates of Acetylcholinesterase Mutants, F295L and F297I by Mono- and Bis-Quarternary Oximes -
Author(s) : Wong L , Radic Z , Hosea NA , Berman HA , Taylor P
Ref : In: Structure and Function of Cholinesterases and Related Proteins - Proceedings of Sixth International Meeting on Cholinesterases , (Doctor, B.P., Taylor, P., Quinn, D.M., Rotundo, R.L., Gentry, M.K. Eds) Plenum Publishing Corp. :250 , 1998
PubMedID: