46. Liang, S.; Li, L.; Hsu, W-L; Uversky, V.; Zhou, Y.; Dunker, A. K.; Meroueh, S. O. Molecular Design of Protein Interaction Sites with a New Algorithm that Incorporates Receptor Flexibility J. Mol. Biol. (2008). Submitted

45. Liang, S.; Meroueh S. O.; Zhou Yaoqi Enriching near-native structures from protein-protein docking decoys using an empirical scoring function. Bioinformatics (2008) Submitted

44. Shi, Q.; Meroueh, S. O.; Fisher, J.; Mobashery S. Investigation of the Mechanism of the Cell Wall DD-Carboxypeptidase Reaction of Penicillin-Binding Protein 5 of Escherichia coli by QM/MM Calculations JACS (2008) In Press

43. Jewell, J.; Oh, E.; Bennett, S. M.; Meroueh, S. O., and Thurmond, D. The tyrosine phosphorylation of Munc18c induces a switch in binding specificity from syntaxin 4 to Doc2beta J. Biol. Chem. (2008). In Press

42. Li, Liwei and Meroueh, S. O. Receptor-Ligand Interactions in Biological Systems. In: Encyclopedia for the Life Sciences. John Wiley & Sons. London (2008) In press

41. Li, Liwei; O’Callaghan, B. J.; Dantzer, J. J. and Meroueh S. O. PDBcal: A Comprehensive Dataset for Receptor-Ligand Interactions with Three-Dimensional structures and Binding Thermodynamics from Isothermal Titration Calorimetry. Chem. Biol. & Drug Design. (2008) 71:529-32.

40. Samy Meroueh: Normal Mode Analysis Theoretical and Applications to Biological and Chemical Systems. Briefings in Bioinformatics 8(5): 378-379 (2007)

39. Li, Liwei; Uversky N. V.; Dunker, K. A.; Meroueh, S. O. A Computational Investigation of Allostery in the Catabolite Activator Protein. J. Am. Chem. Soc. (2007) 129(50), 15668-76

38. Zhang, W.; Shi, Q.; Meroueh, S. O.; Vakulenko, S. B.; Mobashery, S., Catalytic Mechanism of Penicillin-Binding Protein 5 of Escherichia coli. J. Biol. Chem. 2007, 46, 10113-10121.

37. Rosenblum, G.*; Meroueh, S.*; Toth, M.; Fisher, J. F.; Fridman, R.; Mobashery, S.; Sagi, I. Molecular Structures and Dynamics of the Stepwise Activation of a Matrix Metalloproteinase Zymogen: Challenging the Cysteine Switch Dogma, J. Am. Chem. Soc. 2007 129(44),13566-74. (Authors contributed equally)

36. Meroueh, S. O. and Mobashery, S., Conformational Transition in the Aminoacyl t-RNA Site of the Bacterial Robosome both in the Presence and Absence of an Aminoglycoside Antibiotic. Chemical Biology and Drug Design 2007, 69, (5), 291-297.

35. Meroueh, S. O.; Cha, J.; Mobashery, S. Inhibition of Class A ß-Lactamases, In Enzyme-Mediated Resistance to Antibiotics: Mechanisms, Dissemination, and Prospects for Inhibition, Bonomo, R. A.; Tolmasky, M. E., Eds.; ASM Press, 2007, pp101-114, Washington D.C.

34. Li, J.; Cross, J. B.; Vreven, T.; Meroueh, S. O. ; Mobashery, S.; Schlegel, H. B., Lysine Carboxylation in Proteins: OXA-10 Beta-Lactamase. Proteins 2005, 61, (2), 246-257.

33. Osenkowski, P.; Meroueh, S. O. ; Pavel, D.; Mobashery, S.; Fridman, R., Mutational and Structural Analyses of the Hinge Region of Membrane Type 1-Matrix Metalloproteinase and Enzyme Processing. J. Biol. Chem. 2005, 280, (28), 26160-26168.

32. Murray, J. B.; Meroueh, S. O.; Russell, R. J.; Lentzen, G.; Haddad, J.; Mobashery, S., Interactions of Designer Antibiotics and the Bacterial Ribosomal Aminoacyl-tRNA Site. Chem. Biol. 2006, 13, (2), 129-38.

31. Hesek, D.; Toth, M.; Meroueh, O.; Brown, S.; Zhao, H.; Sakr, W.; Fridman, R.; Mobashery, S., Design and Characterization of a Metalloproteinase Inhibitor-Tethered Resin for the Detection of Active MMPs in Biological Samples. Chem. Biol. 2006, 13, 379-388.

30. Meroueh, S. O.; Bencze, K. Z.; Hesek, D.; Lee, M.; Fisher, J. F.; Stemmler, T. L.; Mobashery, S., Three-Dimensional Structure of the Bacterial Cell Wall Peptidoglycan. Proc. Natl. Acad. Sci. USA 2006, 103, (12), 4404-4409.

29. Fisher, J. F.; Meroueh, S. O.; Mobashery, S., Nanomolecular and Supramolecular Paths toward the Bacterial Peptidoglycan Structure. Microbe 2006, 1, 420-427.

28. Rekharsky, M.; Hesek, D.; Lee, M.; Meroueh, S. O.; Inoue, Y.; Mobashery, S., Thermodynamics of interactions of vancomycin and synthetic surrogates of bacterial cell wall. J. Am. Chem. Soc. 2006, 128, (24), 7736-7737.

27. Cross, J. B.; Vreven, T.; Meroueh, S. O.; Mobashery, S.; Schlegel, H. B., Computational Investigation of Irreversible Inactivation of the Zinc-Dependent Protease Carboxypeptidase A. J. Phys. Chem. B 2005, 109, (10), 4761-4769.

26. Fisher, J. F.; Meroueh, S. O.; Mobashery, S., Bacterial Resistance to Beta-Lactam Antibiotics: Compelling Opportunism, Compelling Opportunity. Chem. Rev. 2005, 105, (2), 395-424.

25. Ikejiri, M.; Bernardo, M. M.; Meroueh, S. O. ; Brown, S.; Chang, M.; Fridman, R.; Mobashery, S., Design, Synthesis, and Evaluation of a Mechanism-Based Inhibitor for Gelatinase A. J. Org. Chem. 2005, 70, (14), 5709-5712.

24. Lee, M.; Bernardo, M. M.; Meroueh, S. O. ; Brown, S.; Fridman, R.; Mobashery, S., Synthesis of Chiral 2-(4-Phenoxyphenylsulfonylmethyl)-Thiiranes as Selective Gelatinase Inhibitors. Org. Lett. 2005, 7, (20), 4463-4465.

23. Meroueh, S. O. ; Fisher, J. F.; Schlegel, H. B.; Mobashery, S., Ab initio QM/MM Study of Class A Beta-Lactamase Acylation: Dual Participation of Glu166 and Lys73 in a Concerted Base Promotion of Ser70. J. Am. Chem. Soc. 2005, 127, (44), 15397-15407.

22. Toth, M.; Osenkowski, P.; Hesek, D.; Brown, S.; Meroueh, S. O. ; Sakr, W.; Mobashery, S.; Fridman, R., Cleavage at the Stem Region Releases an Active Ectodomain of the Membrane Type 1 Matrix Metalloproteinase. Biochem. J. 2005, 387, 497-506.

21. Birck, C.; Cha, J. Y.; Cross, J.; Schulze-Briese, C.; Meroueh, S. O.; Schlegel, H. B.; Mobashery, S.; Samama, J. P., 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. J. Am. Chem. Soc. 2004, 126, (43), 13945-13947.

20. Brown, S.; Meroueh, S. O.; Fridman, R.; Mobashery, S., Quest for Selectivity in Inhibition of Matrix Metalloproteinases. Curr. Top. Med. Chem. 2004, 4, (12), 1227-1238.

19. Golemi-Kotra, D.; Meroueh, S. O.; Kim, C.; Vakulenko, S. B.; Bulychev, A.; Stemmler, A. J.; Stemmler, T. L.; Mobashery, S., 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. 2004, 279, (33), 34665-34673.

18. Kim, C.; Haddad, J.; Vakulenko, S. B.; Meroueh, S. O.; Wu, Y.; Yan, H.; Mobashery, S., Fluorinated Aminoglycosides and their Mechanistic Implication for Aminoglycoside 3 '-Phosphotransferases from Gram-Negative Bacteria. Biochemistry 2004, 43, (9), 2373-2383.

17. Fridman, R.; Toth, M.; Chvyrkova, I.; Meroueh, S. O.; Mobashery, S., Cell Surface Association of Matrix Metalloproteinase-9 (Gelatinase B). Cancer and Metastasis Rev 2003, 22, (2-3), 153-166.

16. Golemi-Kotra, D.; Cha, J. Y.; Meroueh, S. O.; Vakulenko, S. B.; Mobashery, S., Resistance to Beta-Lactam Antibiotics and its Mediation by the Sensor Domain of the Transmembrane BlaR Signaling Pathway in Staphylococcus aureus. J. Biol. Chem. 2003, 278, (20), 18419-18425.

15. Meroueh, S. O.; Minasov, G.; Lee, W.; Shoichet, B. K.; Mobashery, S., Structural Aspects for Evolution of Beta-Lactamases from Penicillin-Binding Proteins. J. Am. Chem. Soc. 2003, 125, (32), 9612-9618.

14. Rosenblum, G.; Meroueh, S. O.; Kleifeld, O.; Brown, S.; Singson, S. P.; Fridman, R.; Mobashery, S.; Sagi, I., Structural Basis for Potent Slow Binding Inhibition of Human Matrix Metalloproteinase-2 (MMP-2). J. Biol. Chem. 2003, 278, (29), 27009-27015.

13. Song, K. Y.; Meroueh, O.; Hase, W. L., Dynamics of Cr(CO)(6)(+) Collisions with Hydrogenated Surfaces. J. Chem. Phys. 2003, 118, (6), 2893-2902.

12. Wang, J. P.; Meroueh, S. O.; Wang, Y. F.; Hase, W. L., Efficiency of Energy Transfer in Protonated Diglycine and Dialanine SID - Effects of Collision Angle, Peptide Ion Size, and Intramolecular Potential. Int. J. Mass. Spectrom. 2003, 230, (1), 57-64.

11. Wilkinson, A. S.; Bryant, P. K.; Meroueh, S. O.; Page, M. G. P.; Mobashery, S.; Wharton, C. W., 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 2003, 42, (7), 1950-1957.

10. Maveyraud, L.; Golemi-Kotra, D.; Ishiwata, A.; Meroueh, O.; Mobashery, S.; Samama, J. P., High-Resolution X-ray Structure of an Acyl-Enzyme Species for the Class D OXA-10 Beta-Lactamase. J. Am. Chem. Soc. 2002, 124, (11), 2461-2465.

9. Meroueh, O.; Hase, W. L., Dynamics of Energy Transfer in Peptide-Surface Collisions. J. Am. Chem. Soc. 2002, 124, (7), 1524-1531.

8. Meroueh, S. O.; Roblin, P.; Golemi, D.; Maveyraud, L.; Vakulenko, S. B.; Zhang, Y.; Samama, J. P.; Mobashery, S., Molecular Dynamics at the Root of Expansion of Function in the M69L Inhibitor-Resistant TEM Beta-Lactamase from Escherichia coli. J. Am. Chem. Soc. 2002, 124, (32), 9422-9430.

7. Meroueh, S. O.; Wang, Y. F.; Hase, W. L., Direct Dynamics Simulations of Collision- and Surface-Induced Dissociation of N-Protonated Glycine. Shattering Fragmentation. J. Phys. Chem. A 2002, 106, (42), 9983-9992.

6. 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.; Fridman, R., Complex Pattern of Membrane type 1 Matrix Metalloproteinase Shedding - Regulation by Autocatalytic Cell Surface Inactivation of Active Enzyme. J. Biol. Chem. 2002, 277, (29), 26340-26350.

5. Meroueh, O.; Hase, W. L., Effect of Surface Stiffness on the Efficiency of Surface-Induced Dissociation. Phys. Chem. Chem. Phys. 2001, 3, (12), 2306-2314.

4. Sun, L. P.; Claire, P. D.; Meroueh, O.; Hase, W. L., Dynamics of Ar+CH4/Ni{111} Collision-Induced Desorption. J. Chem. Phys. 2001, 114, (1), 535-544.

3. Meroueh, O.; Hase, W. L., Energy Transfer Pathways in the Collisional Activation of Peptides. Int. J. Mass. Spectrom. 2000, 201, (1-3), 233-244.

2. Sawilowsky, E. F.; Meroueh, O.; Schlegel, H. B.; Hase, W. L., Structures, Energies, and Electrostatics for Methane Complexed with Alumina clusters. J. Phys. Chem. A 2000, 104, (21), 4920-4927.

1. Meroueh, O.; Hase, W. L., Collisional Activation of Small Peptides. J. Phys. Chem. A 1999, 103, (20), 3981-3990.