Molecular level activation insights from a NR2A/NR2B agonist

Journal of Biomolecular Structure and Dynamics

Volumn 32, Issue 5, 2014, Pages 683-693

  Ieongtou, Weng ^a   Chang, Su Sen ^b   Wu, Dongchuan ^b,c   Lai, Ted Weita ^b,c   Wang, Yu Tian ^b,d   Hsu, Chung Y ^c   Yu Chianchen, Calvin ^b,c,e,f  

^a CHINA MEDICAL UNIVERSITY   (Taiwan)

^b CHINA MEDICAL UNIVERSITY HOSPITAL   (Taiwan)

^c CHINA MEDICAL UNIVERSITY   (Taiwan)

^d UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^e ASIA UNIVERSITY   (Taiwan)

^f CHINA MEDICAL UNIVERSITY BEIGANG HOSPITAL   (Taiwan)

Author keywords

Alliin; molecular dynamics (MD); N methyl D aspartate receptors (NMDAR); traditional Chinese medicine (TCM)

Indexed keywords

ALLIIN; N METHYL DEXTRO ASPARTIC ACID RECEPTOR 2A; N METHYL DEXTRO ASPARTIC ACID RECEPTOR 2B; CYSTEINE; N METHYL DEXTRO ASPARTIC ACID RECEPTOR; N-METHYL D-ASPARTATE RECEPTOR SUBTYPE 2A; NR2B NMDA RECEPTOR;

ARTICLE; BINDING AFFINITY; BINDING SITE; BIOLOGICAL ACTIVITY; CONTROLLED STUDY; DRUG PROTEIN BINDING; ELECTROPHYSIOLOGY; EMBRYO; HUMAN; HUMAN CELL; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; AGONISTS; ANALOGS AND DERIVATIVES; CHEMICAL DATABASE; CHEMISTRY; CHINESE MEDICINE; HEK293 CELL LINE; METABOLISM; PATCH CLAMP TECHNIQUE;

CYSTEINE; DATABASES, CHEMICAL; HEK293 CELLS; HUMANS; MEDICINE, CHINESE TRADITIONAL; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; PATCH-CLAMP TECHNIQUES; PROTEIN CONFORMATION; RECEPTORS, N-METHYL-D-ASPARTATE;

EID: 84896691613     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2013.787371     Document Type: Article

References (40)

1. Andersen, H. C. (1983). Rattle: A velocity version of the shake algorithm for molecular dynamics calculations. Journal of Computational Physics, 52, 24-34.
2. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., &, Karplus, M. (1983). Journal of Computational Chemistry, 4, 187-217.
3. Chang, S. S., Huang, H.-J., &, Chen, C. Y.-C. (2011). Two birds with one stone? Possible dual-targeting H1N1 inhibitors from traditional Chinese medicine. PLoS Computational Biology, 7, e1002315.
4. Chen, C. Y.-C. (2011). TCM database@Taiwan: The worlds largest traditional Chinese medicine database for drug screening in silico. PLoS ONE, 6, e15939.
5. Chen, C. Y.-C. (2013). When modern computational systems biology meets traditional Chinese medicine. In James D. Adams, & Eric J. Lien (Eds.), Traditional Chinese medicine: Scientific basis for its use (pp. 61-80). London: Royal society of chemisty.
6. Chen, K. C., &, Chen, C. Y. C. (2011). Soft Matter, 7, 4001-4008.
7. Costa, B. M., Irvine, M. W., Fang, G., Eaves, R. J., Mayo-Martin, M. B., Skifter, D. A.,., Monaghan, D. T. (2010). Journal of Pharmacology and Experimental Therapeutics, 335, 614-621.
8. Danbolt, N. C. (2001). Progress in Neurobiology, 65, 1-105.
9. Discovery Studio Modeling Environment v. 2.5 (Accelerys Software Inc., San Diego, 2009).
10. Fairfield, J. (1983). IEEE T Pattern Analysis, 5, 104-110.
11. Fletcher, R. (1969). Optimization. New York, NY: Academic Press.
12. Fletcher, R., &, Reeves, C. M. (1964). The Computer Journal, 7, 149-154.
13. Furukawa, H., Singh, S. K., Mancusso, R., &, Gouaux, E. (2005). Nature, 438, 185-192.
14. Ginalski, K. (2006). Current Opinion in Structural Biology, 16, 172-177.
15. Hammonds, K. D., &, Ryckaert, J. P. (1991). Computer Physics Communications, 62, 336-351.
16. Jin, R., Banke, T. G., Mayer, M. L., Traynelis, S. F., &, Gouaux, E. (2003). Nature Neuroscience, 6, 803-810.
17. Kabsch, W., &, Sander, C. (1983). Biopolymers, 22, 2577-2637.
18. Kolaskar, A. S., &, Sawant, S. (1996). International Journal of Peptide and Protein Research, 47, 110-116.
19. Lee, J. M., Zipfel, G. J., &, Choi, D. W. (1999). Nature, 399, A7-14.
20. Lim-Wilby, M., Jiang, J., Waldman, M., &, Venkatachalam, C. M. (2002). Abstract of Papers American Chemical Society, 224, U345-U345.
21. Lin, T. L., &, Song, G. (2011). Proteins, 79, 2475-2490.
22. Lipton, S. A., &, Rosenberg, P. A. (1994). New England Journal of Medicine, 330, 613-622.
23. Liu, J., Wu, D. C., &, Wang, Y. T. (2010). Nature Neuroscience, 13, 1225-1232.
24. Lovell, S. C., Davis, I. W., Arendall, W. B., de Bakker, P. I. W., Word, J. M., Prisant, M. G.,., Richardson, D. C. (2002). Proteins: Structure. Function & Genetics, 50, 437-450.
25. Magrane, M., & Consortium, U. (2011). Database 2011, 10.1093/database/bar1009.
26. Martin, H. G., &, Wang, Y. T. (2010). Cell, 140, 174-176.
27. Pinto, F. D., &, Freitas, C. M. D. (2011). Visual Computer, 27, 463-472.
28. Rothman, S. M., &, Olney, J. W. (1995). Trends in Neurosciences, 18, 57-58.
29. Simon, R. P., Swan, J. H., Griffiths, T., &, Meldrum, B. S. (1984). Science, 226, 850-852.
30. Sun, Y., Olson, R., Horning, M., Armstrong, N., Mayer, M., &, Gouaux, E. (2002). Nature, 417, 245-253.
31. Tou, W. I., Chang, S. S., Lee, C. C., &, Chen, C. Y. (2013). Science Report-UK, 3, 844.
32. Tou, W. I., &, Chen, C. Y.-C. (2012). In silico investigation of potential Src kinase ligands from traditional Chinese medicine. PLoS ONE, 7, e33728.
33. Tsai, T. Y., Chang, K. W., &, Chen, C. Y. (2011). Journal of Computer-Aided Molecular Design, 25, 525-531.
34. Tu, W., Xu, X., Peng, L., Zhong, X., Zhang, W., Soundarapandian, M. M.,., Lu, Y. (2010). Cell, 140, 222-234.
35. Venkatachalam, C. M., Jiang, X., Oldfield, T., &, Waldman, M. (2003). Journal of Molecular Graphics and Modelling, 21, 289-307.
36. Weston, M. C., Schuck, P., Ghosal, A., Rosenmund, C., &, Mayer, M. L. (2006). Nature Structural & Molecular Biology, 13, 1120-1127.
37. Wuthrich, K. (1990). Current Science India, 59, 825-831.
38. The National Institute of Neurological Disorders and Stroke rt-PA Stroke Study Group. (1995). The New England Journal of Medicine, 333, 1581-1587.
39. Yang, S.-C., Chang, S.-S., Chen, H.-Y., &, Chen, C. Y.-C. (2011). Identification of potent EGFR inhibitors from TCM Database@Taiwan. PLoS Computational Biology, 7, e1002189.
40. Zhou, L., Li, F., Xu, H. B., Luo, C. X., Wu, H. Y., Zhu, M. M.,., Zhu, D. Y. (2010). Nature Medicine, 16, 1439-1443.