Parameterization of aromatic azido groups: Application as photoaffinity probes in molecular dynamics studies

Journal of Molecular Modeling

Volumn 15, Issue 11, 2009, Pages 1291-1297

  Pieffet, Gilles ^a   Petukhov, Pavel A ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

Azido groups; Force field; Molecular dynamics; Molecular mechanics; Parameterization; Photoaffinity probes

Indexed keywords

ALIPHATIC COMPOUND; AMBER; AROMATIC COMPOUND; AZIDE; HISTONE DEACETYLASE;

ARTICLE; CHEMICAL ANALYSIS; CHEMICAL BINDING; CHEMICAL STRUCTURE; CONTROLLED STUDY; DENSITY FUNCTIONAL THEORY; GEOMETRY; MATHEMATICAL COMPUTING; MATHEMATICAL PARAMETERS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULAR PROBE; PHOTOAFFINITY LABELING; PRIORITY JOURNAL; SIMULATION;

AZIDES; COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR PROBES; PHOTOAFFINITY LABELS; ROTATION; SURFACE PROPERTIES;

EID: 70349250000     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-009-0488-z     Document Type: Article

References (28)

1. He B et al (2009) Photolabeling probes for mapping the multiple binding poses of HDAC inhibitors. In: Abstract of papers of AACR-ACS Chemistry in Cancer Research: A Vital Partnership in Cancer Drug Discovery and Development. New Orleans, LA, p A5
2. Kouzarides T (1999) Histone acetylases and deacetylases in cell proliferation. Curr Opin Genet Dev 9:40-48
3. Archer SY, Hodin RA (1999) Histone acetylation and cancer. Curr Opin Genet Dev 9:171-174
4. Cress WD, Seto E (2000) Histone deacetylases, transcriptional control, and cancer. J Cell Physiol 184:1-16
5. Mahlknecht U, Ottmann OG, Hoelzer D (2000) When the band begins to play: histone acetylation caught in the crossfire of gene control. Mol Carcinog 27:268-271
6. Hahnen E et al (2008) Histone deacetylase inhibitors: Possible implications for neurodegenerative disorders. Expert Opin Investig Drugs 17:169-184
7. Kozikowski AP et al (2007) Functional differences in epigenetic modulators - superiority of mercaptoacetamide-based histone deacetylase inhibitors relative to hydroxamates in cortical neuron neuroprotection studies. J Med Chem 50:3054-3061
8. Carvalho ATP, Fernandes PA, Ramos MJ (2007) Parameterization of AZT - a widely used nucleoside inhibitor of HIV-1 reverse transcriptase. Int J Quantum Chem 107:292-298
9. Cornell WD et al (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179-5197
10. Wang J et al (2004) Development and testing of a general amber force field. J Comput Chem 25:1157-1174
11. Dennington R II et al (2003) GaussView. Semichem Inc, Shawnee Mission, KS
12. Frisch MJ et al (2004) Gaussian 03, Revision C.02. Gaussian Inc, Wallingford, CT
13. Berendsen HJC, Spoel Dvd, Drunen Rv (1995) GROMACS: A message-passing parallel molecular dynamics implementation. Comp Phys Commun 91:43-56
14. Lindal E, Hess B, Spoel Dvd (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis. J Mol Model 7:306-317
15. van der Spoel D et al (2001) Gromacs User Manual Version 3.0. Nijenborgh, Groningen, Netherlands. Internet: http://www.gromacs.org
16. van der Spoel D et al (2005) Gromacs: Fast, flexible and free. J Comput Chem 26:1701-1718
17. Wang J et al (2006) Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graphics Modell 25:247-260
18. Sorin EJ, Rhee YM, Pande VS (2005) Does water play a structural role in the folding of small nucleic acids? Biophys J 88:2516-2524
19. Jorgensen WL et al (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935
20. Hess B et al (1997) LINCS: A linear constraint solver for molecular simulations. J Comput Chem 18:1463-1472
21. Miyamoto S, Kollman PA (1992) SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comput Chem 13:952-962
22. Berendsen HJC et al (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690
23. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems. J Chem Phys 98:10089-10092
24. Anderson DWW, Rankin DWH, Robertson A (1972) Electron diffraction determination of the molecular structures of methylazide, methylisocyanate and methylisothiocyanate in the gas phase. J Mol Structure 14:385-396
25. Winnewisser BP (1980) The substitution structure of hydrazoic acid, HNNN. J Mol Spectrosc 82:220-223
26. Klaeboe P et al (1986) The vibrational spectra, molecular structure and conformation of organic azides. Part I. A survey. J Mol Struct 141:161-172
27. McQuaid MJ, Sun H, Rigby D (2004) Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains. J Comput Chem 25:61-71
28. Cross JB et al (2002) The active site of a zinc-dependent metalloproteinase influences the computed pK(a) of ligands coordinated to the catalytic zinc ion. J Am Chem Soc 124:11004-11007