Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: Affinity and conformation

Biophysical Chemistry

Volumn 78, Issue 1-2, 1999, Pages 183-193

  Luo, Ray ^a   Head, Martha S ^a,b   Given, James A ^a   Gilson, Michael K ^a,b  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROFORM; N METHYLACETAMIDE; NUCLEIC ACID BASE;

ALGORITHM; BINDING AFFINITY; CALCULATION; COMPUTER SIMULATION; CONFERENCE PAPER; DIELECTRIC CONSTANT; DRUG STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL;

ACETAMIDES; ALGORITHMS; BASE PAIRING; CHEMISTRY, PHYSICAL; CHLOROFORM; COMPUTER SIMULATION; ENERGY TRANSFER; HYDROGEN BONDING; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS;

EID: 0033043720     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(98)00229-4     Document Type: Conference Paper

References (47)

1. Ajay, M.A. Murcko, J. Med. Chem. 38 (1995) 4953-14496.
2. Gilson M.K., Given J.A., Bush B.L., McCammon J.A. Biophys. J. 72:1997;1047-1069.
3. Lesyng B., Saenger W. Carbohydr. Res. 133:1984;187-197.
4. Lipkowitz K.B., Demeter D.A., Zegarra R., Larter R., Darden T. J. Am. Chem. Soc. 110:1988;3446-3452.
5. Lipkowitz K.B., Zegarra R. J. Comput. Chem. 10:1989;595-602.
6. Head M.S., Given J.A., Gilson M.K. J. Phys. Chem. 101:1997;1609-1618.
7. R. Luo, L. David, H. Hung, J. Devaney, M.K. Gilson, J. Phys. Chem., in press.
8. Kolossvary I. J. Phys. Chem. A. 101:1997;9900-9905.
9. Honig B., Sharp K., Yang A.-S. J. Phys. Chem. 97:1993;1101-1109.
10. Sitkoff D., Sharp K.A., Honig B. J. Phys. Chem. 98:1994;1978-1988.
11. Sharp K.A., Nicholls A., Friedman R., Honig B. Biochemistry. 30:1991;9686-9697.
12. Gilson M.K., Sharp K.A., Honig B.H. J. Comp. Chem. 9:1988;327-335.
13. Still W.C., Tempczyk A., Hawley R.C., Hendrickson T. J. Am. Chem. Soc. 112:1990;6127-6129.
14. Gilson M.K., Honig B. J. Comput.-Aided Mol. Des. 5:1990;5-20.
15. Schaefer M., Froemmel C. J. Mol. Biol. 216:1990;1045-1066.
16. Hawkins G.D., Cramer C.J., Truhlar D.G. Chem. Phys. Lett. 246:1995;122-129.
17. Scarsi M., Apostolakis J., Caflisch A. J. Phys. Chem. 101:1997;8098-8106.
18. Qiu D., Shenkin P.S., Hollinger F.P., Still W.C. J. Phys. Chem. 101:1997;3005-3014.
19. McDonald D.Q., Still W.C. J. Am. Chem. Soc. 116:1994;11550-11553.
20. Kolossvary I. J. Am. Chem. Soc. 119:1997;10233-10234.
21. Luo R., Head M.S., Moult J., Gilson M.K. J. Am. Chem. Soc. 120:1998;6138-6146.
22. Bental N., Topol I.A., Yang A., Burt S.K., Honig B. J. Phys. Chem. 101:1997;450-457.
23. Jorgensen W.L. J. Am. Chem. Soc. 111:1989;3770-3771.
24. Sneddon S.F., Tobias D.J., Brooks III C.L. J. Mol. Biol. 209:1989;817-820.
25. Pranata J., Jorgensen W.L. Tetrahedron. 47:1991;2491-2501.
26. Simonson T., Brunger A.T. J. Phys. Chem. 98:1994;4683-4694.
27. Osapay K., Young W.S., Bashford D., Brooks III C.L., Case D.A. J. Phys. Chem. 100:1996;2698-2705.
28. Steinberg I.Z., Scheraga H.A. J. Biol. Chem. 238:1963;172-181.
29. Hill, T.L., An Introduction to Statistical Thermodynamics, Dover, New York, 1986.
30. Jorgensen W.L. J. Am. Chem. Soc. 111:1989;3770-3771.
31. Justice M.-C., Justice J.-C. J. Sol. Chem. 5:1976;543-561.
32. Gilson M.K. Proteins Struct. Funct. Genet. 15:1993;266-282.
33. W.H. Press, B.P. Flannery, S.A. Teukolsky, W.T. Vetterling, Numerical Recipes: The Art of Scientific Computing, Cambridge University Press, London, 1986.
34. Kyogoku Y., Lord R.C., Rich A. J. Am. Chem. Soc. 89:1967;496-504.
35. Davis M.E., Madura J.D., Luty B.A., McCammon J.A. Comput. Phys. Commun. 62:1991;187-197.
36. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. J. Comput. Chem. 4:1983;187-217.
37. MacKerell A.D. Jr., Wiókiewicz-Kuczera J., Karplus M. J. Am. Chem. Soc. 117:1995;11946-11975.
38. Sitkoff D., Ben-Tal N., Honig B. J. Phys. Chem. 100:1996;2744-2752.
39. Giesen D.J., Chambers C.C., Cramer C.J., Truhlar D.G. J. Phys. Chem. 101:1997;2061-2069.
40. Quanta 4.1 Molecular Simulations Inc. San Diego, CA.
41. W. Saenger, Principles of Nucleic Acid Structure, Springer-Verlag, New York, 1984.
42. Mahamadi F., Richards N.G.J., Guida W.C.et al. J. Comput. Chem. 11:1990;440.
43. Binford J.S. Jr., Holloway D.M. J. Mol. Biol. 31:1968;91-99.
44. L. David, R. Luo, M.S. Head, M.K. Gilson, J. Phys. Chem., in press.
45. Kyogoku Y., Lord R.C., Rich A. Biochim. Biophys. Acta. 179:1969;10-17.
46. Carmona P., Molina M., Lasagabaster A., Escobar R., Altabef A.B. J. Phys. Chem. 97:1993;9519-9524.
47. Krikorian S.E. J. Phys. Chem. 86:1982;1875-1881.