Synchronized conformational fluctuations and binding site desolvation during molecular recognition

Biochemistry

Volumn 43, Issue 49, 2004, Pages 15446-15452

  Jusuf, Sutjano ^a   Axelsen, Paul H ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTICS; COMPUTER SIMULATION; CONFORMATIONS; DIMERIZATION; HYDROGEN BONDS; MOLECULAR DYNAMICS; REACTION KINETICS;

GLYCOPEPTIDE; LIGANDS; MOLECULAR RECOGNITION;

PROTEINS;

ANTIBIOTIC AGENT; GLYCOPEPTIDE; HYDROGEN; VANCOMYCIN; WATER;

ARTICLE; BINDING SITE; CONFORMATION; HYDROGEN BOND; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; SIMULATION; SOLVATION;

AMIDES; ANTI-BACTERIAL AGENTS; BINDING SITES; COMPUTER SIMULATION; DIMERIZATION; DIPEPTIDES; HYDROGEN BONDING; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; SOFTWARE; SOLVENTS; THERMODYNAMICS; VANCOMYCIN; WATER;

EID: 10644274432     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048357t     Document Type: Article

References (24)

1. Israelachvili, J. N. (1992) Intermolecular and Surface Forces, Academic Press, San Diego.
2. Burgen, A. S. V., Roberts, G. C. K., and Feeney, J. (1975) Binding of Flexible Ligands to Macromolecules, Nature 253, 753-755.
3. Popieniek, P. H., and Pratt, R. F. (1991) Kinetics and Mechanism of Binding of Specific Peptides to Vancomycin and Other Glycopeptide Antibiotics, J. Am. Chem. Soc. 113, 2264-2270.
4. Waltho, J. P., Williams, D. H., Stone, D. J. M., and Skelton, N. J. (1988) Intramolecular Determinants of Conformation and Mobility within the Antibiotic Vancomycin, J. Am. Chem. Soc. 110, 5638-5643.
5. Bartels, C., and Karplus, M. (1997) Multidimensional Adaptive Umbrella Sampling: Applications to Main Chain and Side Chain Peptide Conformations, J. Comput. Chem. 18, 1450-1462.
6. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, J. Comput. Chem. 4, 187-217.
7. Li, D., Sreenivasan, U., Juranic, N., Macura, S., Puga, F. J., II, Frohnert, P. M., and Axelsen, P. H. (1997) Simulated Dipeptide Recognition by Vancomycin, J. Mol. Recogn. 10, 73-87.
8. Axelsen, P. H., and Li, D. (1998) A Rational Strategy for Enhancing the Affinity of Vancomycin Towards Depsipeptide Ligands, Bioorg. Med. Chem. 6, 877-881.
9. Axelsen, P. H., and Li, D. (1998) Improved Convergence in Dual-Topology Free Energy Calculations Through the Use of Harmonic Restraints, J. Comput. Chem. 19, 1278-1283.
10. Jusuf, S., Loll, P. J., and Axelsen, P. H. (2002) The Role of Configurational Entropy in Biochemical Cooperativity, J. Am. Chem. Soc. 124, 3490-3491.
11. Jusuf, S., Loll, P. J., and Axelsen, P. H. (2003) Configurational Entropy and Cooperativity between Ligand Binding and Dimerization in Glycopeptide Antibiotics, J. Am. Chem. Soc. 125, 3988-3994.
12. Feller, S. E., Zhang, Y., Pastor, R. W., and Brooks, B. R. (1995) Constant Pressure Molecular Dynamics Simulation: the Langevin Piston Method, J. Chem. Phys. 103, 4613-4621.
13. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of N-Alkanes, J. Comput. Phys. 23, 327-341.
14. Loll, P. J., Bevivino, A. E., Korty, B. D., and Axelsen, P. H. (1997) Simultaneous Recognition of a Carboxylate-Containing Ligand and an Intramolecular Surrogate Ligand in the Crystal Structure of an Asymmetric Vancomycin Dimer, J. Am. Chem. Soc. 119, 1516-1522.
15. Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A., and Rosenberg, J. M. (1992) The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules, J. Comput. Chem. 13, 1011-1021.
16. Bartels, C., Schaefer, M., and Karplus, M. (1999) Determination of Equilibrium Properties of Biomolecular Systems Using Multidimensional Adaptive Umbrella Sampling, J. Chem. Phys. 111, 8048-8067.
17. Schafer, M., Schneider, T. R., and Sheldrick, G. M. (1996) Crystal Structure of Vancomycin, Structure 4, 1509-1515.
18. Loll, P. J., Miller, R., Weeks, C. M., and Axelsen, P. H. (1998) A Ligand-Mediated Dimerization Mode for Vanomycin, Chem. Biol. 5, 293-298.
19. Loll, P. J., Kaplan, J., Selinsky, B. S., and Axelsen, P. H. (1999) Vancomycin Binding to Low-Affinity Ligands: Delineating a Minimum Set of Interactions Necessary for High-Affinity Binding. J. Med. Chem. 42, 4714-4719.
20. Kaplan, J., Korty, B. D., Axelsen, P. H., and Loll, P. J. (2001) The Role of Sugar Residues in Molecular Recognition by Vancomycin, J. Med. Chem. 44, 1837-1840.
21. Beauregard, D. A., Maguire, A. J., Williams, D. H., and Reynolds, P. E. (1997) Semiquantitation of Cooperativity in Binding of Vancomycin Group Antibiotics to Vancomycin Susceptible and Resistant Organisms, Antimicrob. Agents Chemother. 41, 2418-2423.
22. Nicolaou, K. C., Hughes, R., Cho, S. Y., Winssinger, N., Labischinski, H., and Endermann, R. (2001) Synthesis and Biological Evaluation of Vancomycin Dimers with Potent Activity against Vancomycin-Resistant Bacteria: Target-Accelerated Combinatorial Synthesis, Chem.-Eur. J. 7, 3824-3843.
23. Nicolaou, K. C., Cho, S. Y., Hughes, R., Winssinger, N., Smethurst, C., Labischinski, H., and Endermann, R. (2001) Solid-and Solution-Phase Synthesis of Vancomycin and Vancomycin Analogues with Activity against Vancomycin-Resistant Bacteria, Chem-Eur. J. 7, 3798-3823.
24. Axelsen, P. H., Harel, M., Silman, I., and Sussman, J. L. (1994) Structure and Dynamics of the Active Site Gorge of Acetylcholinesterase: Synergistic Use of Molecular Dynamics Simulation and X-ray Crystallography, Protein Sci. 3, 188-197.