Samy Meroueh

Liu, D., Zhou, D., Wang, B., Knabe, W. E., and Meroueh, S. O. (2015) A New Class of Orthosteric uPAR'uPA Small-Molecule Inhibitors Are Allosteric Modulators of the uPAR'Vitronectin Interaction. ACS Chem. Biol. In Press

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Xu, D., Wang, B., and Meroueh, S. O. (2015) Structure-Based Computational Approaches for Small Molecules Targeting Protein-Protein Interactions. Protein-Protein Interactions: Methods and Applications. In Press

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Yan, C., Li, L., Liu, D., Wempe, M., Reigan, P., Hoffman, B., Guin, S., Helfrich, B., Schwartz, M., Ross, D., Meroueh, S. O., and Theodorescu, D. (2014) Discovery and Characterization of Small Molecules targeting Ral GTPase. Nature 515:443-447

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Wang, B., Buckman, C., Li, L., Hurley, T., and Meroueh, S. O. (2014) Enrichment of Chemical Libraries Docked to Protein Conformational Ensembles and Application to Aldehyde Dehydrogenase 2. J. Chem. Inf. Model : 10.1021/CI5002026

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Peng, X., Wang, F., Li, L., Bum-Erdene, K., Xu, D., Wang, B., Sinn, A. A., Pollok, K. E., Sandusky, G. E., Li, L., Turchi, J. J., Jalal, S. I., and Meroueh, S. O. (2014) Exploring a structural protein-drug interactome for new therapeutics in lung cancer. Mol Biosyst 10, 581-591

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Wang, B., Li, L., Hurley, T. D., and Meroueh, S. O. (2013) Molecular Recognition in a Diverse Set of Protein'Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations. J Chem Inf Model 53, 2659-2670

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Mani, T., Wang, F., Knabe, W. E., Sinn, A. L., Khanna, M., Jo, I., Sandusky, G. E., Sledge, G. W., Jr., Jones, D. R., Khanna, R., Pollok, K. E., and Meroueh, S. O. (2013) Small-molecule inhibition of the uPAR.uPA interaction: synthesis, biochemical, cellular, in vivo pharmacokinetics and efficacy studies in breast cancer metastasis. Bioorg Med Chem 21, 2145-2155

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Mani, T., Liu, D., Zhou, D., Li, L., Knabe, W. E., Wang, F., Oh, K., and Meroueh, S. O. (2013) Probing Binding and Cellular Activity of Pyrrolidinone and Piperidinone Small Molecules Targeting the Urokinase Receptor. ChemMedChem 8, 1963-1977

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Zhang, Q., Zeng, S. X., Zhang, Y., Ding, D., Ye, Q., Meroueh, S. O., and Lu, H. (2012) A small molecule Inauhzin inhibits SIRT1 activity and suppresses tumour growth through activation of p53. EMBO Mol. Med. 4, 298-312

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Wang, F., Eric Knabe, W., Li, L., Jo, I., Mani, T., Roehm, H., Oh, K., Li, J., Khanna, M., and Meroueh, S. O. (2012) Design, synthesis, biochemical studies, cellular characterization, and structure-based computational studies of small molecules targeting the urokinase receptor. Bioorgan Med Chem 20, 4760-4773

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Piekarz, A. D., Due, M. R., Khanna, M., Wang, B., Ripsch, M. S., Wang, R., Meroueh, S. O., Vasko, M. R., White, F. A., and Khanna, R. (2012) CRMP-2 peptide mediated decrease of high and low voltage-activated calcium channels, attenuation of nociceptor excitability, and anti-nociception in a model of AIDS therapy-induced painful peripheral neuropathy. Mol. Pain 8, 54

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Wang, F., Li, J., Sinn, A. L., Knabe, W. E., Khanna, M., Jo, I., Silver, J. M., Oh, K., Li, L., and Sandusky, G. E. (2011) Virtual screening targeting the urokinase receptor, biochemical and cell-based studies, synthesis, pharmacokinetic characterization, and effect on breast tumor metastasis. J. Med. Chem. 54, 7193-7205

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Shi, Q., Meroueh, S. O., Fisher, J. F., and Mobashery, S. (2011) A computational evaluation of the mechanism of penicillin-binding protein-catalyzed cross-linking of the bacterial cell wall. J. Am. Chem. Soc. 133, 5274-5283

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Parajuli, B., Kimble-Hill, A. C., Khanna, M., Ivanova, Y., Meroueh, S., and Hurley, T. D. (2011) Discovery of novel regulators of aldehyde dehydrogenase isoenzymes. Chemico-biological interactions 191, 153-158

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Li, L., Wang, B., and Meroueh, S. O. (2011) Support Vector Machine Scoring of Receptor-Ligand Complexes for Virtual Screening of Chemical Libraries. J. Chem. Inf. Model. 51, 2132-2138

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Li, L., Khanna, M., Jo, I., Wang, F., Ashpole, N., Hudmon, A., and Meroueh, S. O. (2011) Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation. J. Chem. Inf. Model. 51, 755-759

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Khanna, M., Wang, F., Jo, I., Knabe, W. E., Wilson, S. M., Li, L., Bum-Erdene, K., Li, J., G, W. S., Khanna, R., and Meroueh, S. O. (2011) Targeting multiple conformations leads to small molecule inhibitors of the uPAR.uPA protein-protein interaction that block cancer cell invasion. ACS Chem Biol 6, 1232-1243

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Khanna, M., Chelladurai, B., Gavini, A., Li, L., Shao, M., Courtney, D., Turchi, J. J., Matei, D., and Meroueh, S. (2011) Targeting ovarian tumor cell adhesion mediated by tissue transglutaminase. Mol. Cancer Ther. 10, 626-636

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Brittain, J. M., Duarte, D. B., Wilson, S. M., Zhu, W., Ballard, C., Johnson, P. L., Liu, N., Xiong, W., Ripsch, M. S., Wang, Y., Fehrenbacher, J. C., Fitz, S. D., Khanna, M., Park, C. K., Schmutzler, B. S., Cheon, B. M., Due, M. R., Brustovetsky, T., Ashpole, N. M., Hudmon, A., Meroueh, S. O., Hingtgen, C. M., Brustovetsky, N., Ji, R. R., Hurley, J. H., Jin, X., Shekhar, A., Xu, X. M., Oxford, G. S., Vasko, M. R., White, F. A., and Khanna, R. (2011) Suppression of inflammatory and neuropathic pain by uncoupling CRMP-2 from the presynaptic Ca(2)(+) channel complex. Nat. Med. 17, 822-829

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Wang, Y., Brittain, J. M., Jarecki, B. W., Park, K. D., Wilson, S. M., Wang, B., Hale, R., Meroueh, S. O., Cummins, T. R., and Khanna, R. (2010) In silico docking and electrophysiological characterization of lacosamide binding sites on collapsin response mediator protein-2 identifies a pocket important in modulating sodium channel slow inactivation. J. Biol. Chem. 285, 25296-25307

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Li, L., Li, J., Khanna, M., Jo, I., Baird, J. P., and Meroueh, S. O. (2010) Docking Small Molecules to Predicted Off-Targets of the Cancer Drug Erlotinib Leads to Inhibitors of Lung Cancer Cell Proliferation with Suitable In vitro Pharmacokinetic Properties. ACS. Med. Chem. Lett. 1, 229-233

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Li, L., Bum-Erdene, K., Baenziger, P. H., Rosen, J. J., Hemmert, J. R., Nellis, J. A., Pierce, M. E., and Meroueh, S. O. (2010) BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome. Nucleic Acids Res. 38, D765-773

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Xue, B., Li, L., Meroueh, S. O., Uversky, V. N., and Dunker, A. K. (2009) Analysis of structured and intrinsically disordered regions of transmembrane proteins. Molecular Biosystems 5, 1688-1702

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Matute, J. D., Arias, A. A., Wright, N. A., Wrobel, I., Waterhouse, C. C., Li, X. J., Marchal, C. C., Stull, N. D., Lewis, D. B., Steele, M., Kellner, J. D., Yu, W., Meroueh, S. O., Nauseef, W. M., and Dinauer, M. C. (2009) A new genetic subgroup of chronic granulomatous disease with autosomal recessive mutations in p40 phox and selective defects in neutrophil NADPH oxidase activity. Blood 114, 3309-3315

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Liang, S., Meroueh, S. O., Wang, G., Qiu, C., and Zhou, Y. (2009) Consensus scoring for enriching near-native structures from protein-protein docking decoys. Proteins 75, 397-403

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Liang, S., Li, L., Hsu, W. L., Pilcher, M. N., Uversky, V., Zhou, Y., Dunker, A. K., and Meroueh, S. O. (2009) Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. Biochemistry 48, 399-414

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Li, L., Liang, S., Pilcher, M. M., and Meroueh, S. O. (2009) Incorporating receptor flexibility in the molecular design of protein interfaces. Protein Eng. Des. Sel. 22, 575-586

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Shi, Q., Meroueh, S. O., Fisher, J. F., and Mobashery, S. (2008) 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. J. Am. Chem. Soc. 130, 9293-9303

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Li, L., and Meroueh, S. O. (2008) Receptor-Ligand Interactions in Biological Systems. in Encyclopedia for the Life Sciences, John Wiley and Sons, London. pp p. 19

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Li, L., Dantzer, J. J., Nowacki, J., O'Callaghan, B. J., and Meroueh, S. O. (2008) PDBcal: a comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry. Chem. Biol. Drug. Des. 71, 529-532

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Jewell, J. L., Oh, E., Bennett, S. M., Meroueh, S. O., and Thurmond, D. C. (2008) The Tyrosine Phosphorylation of Munc18c Induces a Switch in Binding Specificity from Syntaxin 4 to Doc2{beta}. J. Biol. Chem. 283, 21734-21746

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Zhang, W., Shi, Q., Meroueh, S. O., Vakulenko, S. B., and Mobashery, S. (2007) Catalytic mechanism of penicillin-binding protein 5 of Escherichia coli. Biochemistry 46, 10113-10121

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Rosenblum, G., Meroueh, S., Toth, M., Fisher, J. F., Fridman, R., Mobashery, S., and Sagi, I. (2007) Molecular structures and dynamics of the stepwise activation mechanism of a matrix metalloproteinase zymogen: challenging the cysteine switch dogma. J. Am. Chem. Soc. 129, 13566-13574

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Meroueh, S. O., and Mobashery, S. (2007) Conformational transition in the aminoacyl t-RNA site of the bacterial ribosome both in the presence and absence of an aminoglycoside antibiotic. Chem. Biol. Drug. Des. 69, 291-297

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Meroueh, S. O., Cha, J. Y., and Mobashery, S. (2007) Inhibition of Class A beta-Lactamases. in Enzyme-Mediated Resistance to Antibiotics: Mechanisms, Dissemination, and Prospects for Inhibition (Bonomo, R. A. ed.), ASM Press, Washington D. C. pp

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Li, L., Uversky, V. N., Dunker, A. K., and Meroueh, S. O. (2007) A computational investigation of allostery in the catabolite activator protein. J. Am. Chem. Soc. 129, 15668-15676

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Rekharsky, M., Hesek, D., Lee, M., Meroueh, S. O., Inoue, Y., and Mobashery, S. (2006) Thermodynamics of interactions of vancomycin and synthetic surrogates of bacterial cell wall. J. Am. Chem. Soc. 128, 7736-7737

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Rahaman, A., Song, H., Wang, A. X., Meroueh, S. O., and Hase, W. L. (2006) Chemical Dynamics Simulations of Energy Transfer and Unimolecular Decomposition in Collision-Induced Dissociation (CID) and Surface-Induced Dissociation (SID). in Principles of Mass Spectrometry Applied to Biomolecules (Litschitz, C., and Laskin, J. eds.), Wiley, New York. pp 379-432

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Murray, J. B., Meroueh, S. O., Russell, R. J., Lentzen, G., Haddad, J., and Mobashery, S. (2006) Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site. Chemistry and Biology 13, 129-138

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Meroueh, S. O., Bencze, K. Z., Hesek, D., Lee, M., Fisher, J. F., Stemmler, T. L., and Mobashery, S. (2006) Three-dimensional structure of the bacterial cell wall peptidoglycan. Proceedings of the National Academy of Sciences USA 103, 4404-4409

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Hesek, D., Toth, M., Meroueh, S. O., Brown, S., Zhao, H., Sakr, W., Fridman, R., and Mobashery, S. (2006) Design and characterization of a metalloproteinase inhibitor-tethered resin for the detection of active MMPs in biological samples. Chemistry and Biology 13, 379-386

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Toth, M., Osenkowski, P., Hesek, D., Brown, S., Meroueh, S., Sakr, W., Mobashery, S., and Fridman, R. (2005) Cleavage at the stem region releases an active ectodomain of the membrane type 1 matrix metalloproteinase. Biochemical Journal 387, 497-506

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Osenkowski, P., Meroueh, S. O., Pavel, D., Mobashery, S., and Fridman, R. (2005) Mutational and structural analyses of the hinge region of membrane type 1-matrix metalloproteinase and enzyme processing. J. Biol. Chem. 280, 26160-26168

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Meroueh, S. O., Fisher, J. F., Schlegel, H. B., and Mobashery, S. (2005) Ab initio QM/MM study of class A beta-lactamase acylation: dual participation of Glu166 and Lys73 in a concerted base promotion of Ser70. Journal of the American Chemical Society 127, 15397-15407

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Li, J., Cross, J. B., Vreven, T., Meroueh, S. O., Mobashery, S., and Schlegel, H. B. (2005) Lysine carboxylation in proteins: OXA-10 beta-lactamase. Proteins 61, 246-257

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Lee, M., Bernardo, M. M., Meroueh, S. O., Brown, S., Fridman, R., and Mobashery, S. (2005) Synthesis of chiral 2-(4-phenoxyphenylsulfonylmethyl)thiiranes as selective gelatinase inhibitors. Org. Lett. 7, 4463-4465

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Ikejiri, M., Bernardo, M. M., Meroueh, S. O., Brown, S., Chang, M., Fridman, R., and Mobashery, S. (2005) Design, synthesis, and evaluation of a mechanism-based inhibitor for gelatinase A. J Org Chem 70, 5709-5712

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Fisher, J. F., Meroueh, S. O., and Mobashery, S. (2005) Bacterial resistance to beta-lactam antibiotics: compelling opportunism, compelling opportunity. Chem Rev 105, 395-424

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Cross, J. B., Vreven, T., Meroueh, S. O., Mobashery, S., and Schlegel, H. B. (2005) Computational investigation of irreversible inactivation of the zinc-dependent protease carboxypeptidase A. J Phys Chem B 109, 4761-4769

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Lim, I. T., Meroueh, S. O., Lee, M., Heeg, M. J., and Mobashery, S. (2004) Strategy in inhibition of cathepsin B, a target in tumor invasion and metastasis. Journal of the American Chemical Society 126, 10271-10277

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Kim, C., Haddad, J., Vakulenko, S. B., Meroueh, S. O., Wu, Y., Yan, H., and Mobashery, S. (2004) Fluorinated aminoglycosides and their mechanistic implication for aminoglycoside 3'-phosphotransferases from Gram-negative bacteria. Biochemistry 43, 2373-2383

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Golemi-Kotra, D., Meroueh, S. O., Kim, C., Vakulenko, S. B., Bulychev, A., Stemmler, A. J., Stemmler, T. L., and Mobashery, S. (2004) The importance of a critical protonation state and the fate of the catalytic steps in class A beta-lactamases and penicillin-binding proteins. J. Biol. Chem. 279, 34665-34673

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Brown, S., Meroueh, S. O., Fridman, R., and Mobashery, S. (2004) Quest for selectivity in inhibition of matrix metalloproteinases. Curr. Top. Med. Chem. 4, 1227-1238

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Birck, C., Cha, J. Y., Cross, J., Schulze-Briese, C., Meroueh, S. O., Schlegel, H. B., Mobashery, S., and Samama, J. P. (2004) X-ray crystal structure of the acylated beta-lactam sensor domain of BlaR1 from Staphylococcus aureus and the mechanism of receptor activation for signal transduction. Journal of the American Chemical Society 126, 13945-13947

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Wilkinson, A. S., Bryant, P. K., Meroueh, S. O., Page, M. G., Mobashery, S., and Wharton, C. W. (2003) A dynamic structure for the acyl-enzyme species of the antibiotic aztreonam with the Citrobacter freundii beta-lactamase revealed by infrared spectroscopy and molecular dynamics simulations. Biochemistry 42, 1950-1957

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Wang, J. P., Meroueh, S. O., Wang, Y. F., and Hase, W. L. (2003) Efficiency of energy transfer in protonated diglycine and dialanine SID - Effects of collision angle, peptide ion size, and intramolecular potential. International Journal of Mass Spectrometry 230, 57-64

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Song, K. Y., Meroueh, O., and Hase, W. L. (2003) Dynamics of Cr(CO)(6)(+) collisions with hydrogenated surfaces. J Chem Phys 118, 2893-2902

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Rosenblum, G., Meroueh, S. O., Kleifeld, O., Brown, S., Singson, S. P., Fridman, R., Mobashery, S., and Sagi, I. (2003) Structural basis for potent slow binding inhibition of human matrix metalloproteinase-2 (MMP-2). J. Biol. Chem. 278, 27009-27015

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Meroueh, S. O., Minasov, G., Lee, W., Shoichet, B. K., and Mobashery, S. (2003) Structural aspects for evolution of beta-lactamases from penicillin-binding proteins. Journal of the American Chemical Society 125, 9612-9618

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Golemi-Kotra, D., Cha, J. Y., Meroueh, S. O., Vakulenko, S. B., and Mobashery, S. (2003) Resistance to beta-lactam antibiotics and its mediation by the sensor domain of the transmembrane BlaR signaling pathway in Staphylococcus aureus. J. Biol. Chem. 278, 18419-18425

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Fridman, R., Toth, M., Chvyrkova, I., Meroueh, S. O., and Mobashery, S. (2003) Cell surface association of matrix metalloproteinase-9 (gelatinase B). Cancer Metastasis Rev 22, 153-166

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Toth, M., Hernandez-Barrantes, S., Osenkowski, P., Bernardo, M. M., Gervasi, D. C., Shimura, Y., Meroueh, O., Kotra, L. P., Galvez, B. G., Arroyo, A. G., Mobashery, S., and Fridman, R. (2002) Complex pattern of membrane type 1 matrix metalloproteinase shedding. Regulation by autocatalytic cells surface inactivation of active enzyme. J. Biol. Chem. 277, 26340-26350

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Meroueh, S. O., Wang, Y. F., and Hase, W. L. (2002) Direct dynamics Simulations of collision- and surface-induced dissociation of N-protonated glycine. Shattering fragmentation. Journal of Physical Chemistry A 106, 9983-9992

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Meroueh, S. O., Roblin, P., Golemi, D., Maveyraud, L., Vakulenko, S. B., Zhang, Y., Samama, J. P., and Mobashery, S. (2002) Molecular dynamics at the root of expansion of function in the M69L inhibitor-resistant TEM beta-lactamase from Escherichia coli. Journal of the American Chemical Society 124, 9422-9430

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Meroueh, O., and Hase, W. L. (2002) Dynamics of energy transfer in peptide-surface collisions. Journal of the American Chemical Society 124, 1524-1531

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Maveyraud, L., Golemi-Kotra, D., Ishiwata, A., Meroueh, O., Mobashery, S., and Samama, J. P. (2002) High-resolution X-ray structure of an acyl-enzyme species for the class D OXA-10 beta-lactamase. Journal of the American Chemical Society 124, 2461-2465

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Sun, L. P., Claire, P. D., Meroueh, O., and Hase, W. L. (2001) Dynamics of Ar+CH4/Ni{111} collision-induced desorption. J Chem Phys 114, 535-544

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Meroueh, O., and Hase, W. L. (2001) Effect of surface stiffness on the efficiency of surface-induced dissociation. Physical Chemistry Chemical Physics 3, 2306-2314

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Sawilowsky, E. F., Meroueh, O., Schlegel, H. B., and Hase, W. L. (2000) Structures, energies, and electrostatics for methane complexed with alumina clusters. Journal of Physical Chemistry A 104, 4920-4927

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Meroueh, O., and Hase, W. L. (2000) Energy transfer pathways in the collisional activation of peptides. International Journal of Mass Spectrometry 201, 233-244

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