Molecular dynamics study of molecular mechanism of caffeine and actinocin derivatives interaction with DNA. I. Investigation of monomer and dimer structure of actinocin derivative in ion-hydrate environment
Keywords:
actinocin derivatives, dimerization, hydration, molecular dynamics method, ab initio
Abstract
Interactions of the actinomycin derivative in monomeric and dimeric forms with the ion-hydration environment are studied by the molecular dynamics method. The influence of ions present in the solution for total molecular charge and character of ligand hydration is taken into account. Hydration schemes are in agreement with the experimental data for all systems under consideration. Structures of the most probable forms of the dimers are obtained and stabilizing forces in such complexes are analyzed.
Downloads
Download data is not yet available.
References
1. Данилов В.И., Слюсарчук О. Н., Полтев В.И. и др. // Биополимеры и клетка, 1991,
том 7. №5. с. 5-14
2. Breusegem S.Y., Sadat-Ebrahimi S.E., Douglas K.T. et al // J. Med. Chem. 2001, 44, 2503-2506.
3. AufFinger P., Westhof E. II in Water management in the design and distribution of quality foods. Ross Y.H., Leslie R.B., and Lillford P.J. - editors. Technomic Pulishing Co Inc., Basel. 1999., pp. 165-198
4. Wadkins R.M., Vladu B., Tung Ch.-Sh. // Biochemistry. 1998.V.37. P. 11915-11923.
5. Karawajew L., Glibin E.N., Maleev V.Ya. et al //Anti-Cancer Drug Design. 2000. V.15. P.331-338.
6. Семенов М.А., Гасан А.И., Малеев В.Я. и др. // Вiсн. Харк.ун-ту. №488.Біофізичний Вісник. 2000. Вип.6(1). С. 14-18.
7. Семенов М.А., Сагайдакова Н.И., Больбух Т.В. и др. // Вiсн. Харк.ун-ту. №497. Біофізичний Вісник.. 2000. Вип.2(7). С. 16-23.
8. Auffinger P., Westhof E. // Current Opinion in Structural Biology 1998, V. 8 P. 227-236
9. Cheatham T.E. Ill, Young M.A. // Biopolymers 2000-2001; V. 56, Xs 4, P. 232-256
10. Cornell W.D., Cieplak P., Bayly C.I. et al // J. Amer. Chem. Soc. 117. 5179 (1995).
11. Gasteiger J. and Marsili M. // Tetrahedron, 36, 3219-3288 (1980).
12. Granonovsky Alex A., www http://classic.chem.msu.su/gran/gamess/index.html
13. Schmidt M.W., Baldrige K.K., Boatz J.A. et al // J. Comput. Chem. 1993. V. 14.
P. 1347- 1363
14.Jorgensen W.L., Chandrasekhas J., Madura J. D.., Impey R.W., Klein M.L. // J. Chem. Phys. 79:926-935, 1983.
15. Наберухин Ю.И. // Журн. структур, химии. 1984. Т.25. С. 60-67
16. Malenkov G.G., Tytik D.L., and Zheligovskaya E.A. // J. Mol. Liquids 82 (1999), p. 27-38.
17.Березняк Е.Г., Семенов М.А., Больбух Т.В. и др. // Вiсн. Харк.ун-ту. Направлено в печагь.
18. Зенгер В. Принципы структурной организации нуклеиновых кислот. - М.: Мир, 1987. - 434 с.
19. Круглова Е.Б., Малеев В.Я., Глибин Е.Н., Веселков А.Н. // Вiсн. Харк.ун-ту Направлено в печать.
том 7. №5. с. 5-14
2. Breusegem S.Y., Sadat-Ebrahimi S.E., Douglas K.T. et al // J. Med. Chem. 2001, 44, 2503-2506.
3. AufFinger P., Westhof E. II in Water management in the design and distribution of quality foods. Ross Y.H., Leslie R.B., and Lillford P.J. - editors. Technomic Pulishing Co Inc., Basel. 1999., pp. 165-198
4. Wadkins R.M., Vladu B., Tung Ch.-Sh. // Biochemistry. 1998.V.37. P. 11915-11923.
5. Karawajew L., Glibin E.N., Maleev V.Ya. et al //Anti-Cancer Drug Design. 2000. V.15. P.331-338.
6. Семенов М.А., Гасан А.И., Малеев В.Я. и др. // Вiсн. Харк.ун-ту. №488.Біофізичний Вісник. 2000. Вип.6(1). С. 14-18.
7. Семенов М.А., Сагайдакова Н.И., Больбух Т.В. и др. // Вiсн. Харк.ун-ту. №497. Біофізичний Вісник.. 2000. Вип.2(7). С. 16-23.
8. Auffinger P., Westhof E. // Current Opinion in Structural Biology 1998, V. 8 P. 227-236
9. Cheatham T.E. Ill, Young M.A. // Biopolymers 2000-2001; V. 56, Xs 4, P. 232-256
10. Cornell W.D., Cieplak P., Bayly C.I. et al // J. Amer. Chem. Soc. 117. 5179 (1995).
11. Gasteiger J. and Marsili M. // Tetrahedron, 36, 3219-3288 (1980).
12. Granonovsky Alex A., www http://classic.chem.msu.su/gran/gamess/index.html
13. Schmidt M.W., Baldrige K.K., Boatz J.A. et al // J. Comput. Chem. 1993. V. 14.
P. 1347- 1363
14.Jorgensen W.L., Chandrasekhas J., Madura J. D.., Impey R.W., Klein M.L. // J. Chem. Phys. 79:926-935, 1983.
15. Наберухин Ю.И. // Журн. структур, химии. 1984. Т.25. С. 60-67
16. Malenkov G.G., Tytik D.L., and Zheligovskaya E.A. // J. Mol. Liquids 82 (1999), p. 27-38.
17.Березняк Е.Г., Семенов М.А., Больбух Т.В. и др. // Вiсн. Харк.ун-ту. Направлено в печагь.
18. Зенгер В. Принципы структурной организации нуклеиновых кислот. - М.: Мир, 1987. - 434 с.
19. Круглова Е.Б., Малеев В.Я., Глибин Е.Н., Веселков А.Н. // Вiсн. Харк.ун-ту Направлено в печать.
Published
2002-06-06
Cited
How to Cite
Anischenko, D., E.G. Bereznyak, E., A.V. Shestopalova, A., & Maleev, V. (2002). Molecular dynamics study of molecular mechanism of caffeine and actinocin derivatives interaction with DNA. I. Investigation of monomer and dimer structure of actinocin derivative in ion-hydrate environment. Biophysical Bulletin, 1(10), 36-41. Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/18384
Section
Molecular biophysics
Copyright (c) 2002 Biophysical visnik
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
