SCOPUS 정보 검색 플랫폼

Volumn 30, Issue 4, 2011, Pages 317-328

Addressing the conformational flexibility of serine racemase by combining targeted molecular dynamics, conformational sampling and docking studies

(3) Bruno, Agostino a Amori, Laura a Costantino, Gabriele a

a UNIVERSITY OF PARMA (Italy)

Author keywords

Conformational flexibility; Ensemble docking; Serine racemase; Targeted molecular dynamics

Indexed keywords

LIGANDS; MOLECULAR DYNAMICS;

CONFORMATIONAL FLEXIBILITY; CONFORMATIONAL SAMPLINGS; CONFORMATIONAL STATE; DOCKING STUDIES; ENSEMBLE DOCKING; NMDA RECEPTOR; PLP-DEPENDENT ENZYMES; SERINE RACEMASE; TARGETED MOLECULAR DYNAMICS; X-RAY STRUCTURE;

AMINO ACIDS;

RACEMASE; SERINE; SERINE RACEMASE; UNCLASSIFIED DRUG;

ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME STRUCTURE; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR SYSTEMATICS; PRIORITY JOURNAL; SCREENING; TARGETED MOLECULAR DYNAMIC; X RAY CRYSTALLOGRAPHY;

EID: 79958842174 PISSN: 18681743 EISSN: 18681751 Source Type: Journal
DOI: 10.1002/minf.201000162 Document Type: Article

Times cited : (10)

References (52)

1
- 0033582230
- H. Wolosker, K. N. Sheth, M. Takahashi, J. P. Mothet, R. O. Brady; C. D. Ferris, S. H. Snyder, Proc. Natl. Acad. Sci. USA 1999, 96, 721-725.
- (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 721-725
- Wolosker, H.¹ Sheth, K.N.² Takahashi, M.³ Mothet, J.P.⁴ Brady, R.O.⁵ Ferris, C.D.⁶ Snyder, S.H.⁷

2
- 0037472638
- K. Str ìsovsky, J. Jiràskovà, C. Barinka, P. Majer, B. S. Slusher, J. Konvalinka, FEBS Lett. 2003, 535, 44-48.
- (2003) FEBS Lett. , vol.535 , pp. 44-48
- Strìsovsky, K.¹ Jiràskovà, J.² Barinka, C.³ Majer, P.⁴ Slusher, B.S.⁵ Konvalinka, J.⁶

3
- 19944432442
- V. N. Foltyn, I. Bendikov, J. De Miranda, R. Panizzuti, E. Dumin, M. Shleper, P. Li, M. D. Toney, E. Kartvelishvily, H. Wolosker, J. Biol. Chem. 2005, 280, 1754-1763.
- (2005) J. Biol. Chem. , vol.280 , pp. 1754-1763
- Foltyn, V.N.¹ Bendikov, I.² De Miranda, J.³ Panizzuti, R.⁴ Dumin, E.⁵ Shleper, M.⁶ Li, P.⁷ Toney, M.D.⁸ Kartvelishvily, E.⁹ Wolosker, H.¹⁰

4
- 33646522699
- A. Panatier, D. Theodosis, J. Mothet, B. Touquet, L. Pollegioni, D. Poulain, S. Oliet, Cell 2006, 125, 775-784.
- (2006) Cell , vol.125 , pp. 775-784
- Panatier, A.¹ Theodosis, D.² Mothet, J.³ Touquet, B.⁴ Pollegioni, L.⁵ Poulain, D.⁶ Oliet, S.⁷

5
- 0029020761
- T. Matsui, M. Sekiguchi, A. Hashimoto, U. Tomita, T. Nishikawa, K. Wada, J. Neurochem. 1995, 65, 454-458.
- (1995) J. Neurochem. , vol.65 , pp. 454-458
- Matsui, T.¹ Sekiguchi, M.² Hashimoto, A.³ Tomita, U.⁴ Nishikawa, T.⁵ Wada, K.⁶

6
- 0031046980
- M. J. Schell, Jr. R. O. Brady, M. E. Molliver, S. H. Snyder, J. Neurosci. 1997, 17, 1604-1615.
- (1997) J. Neurosci. , vol.17 , pp. 1604-1615
- Schell, M.J.¹ Brady Jr., R.O.² Molliver, M.E.³ Snyder, S.H.⁴

7
- 77951223140
- M. A. Smith, V. Mack, A. Ebneth, I. Moraes, B. Felicetti, M. Wood, D. Schonfeld, O. Mather, A. Cesura, J. Barker, J. Biol. Chem. 2010, 285, 12873-12881.
- (2010) J. Biol. Chem. , vol.285 , pp. 12873-12881
- Smith, M.A.¹ MacK, V.² Ebneth, A.³ Moraes, I.⁴ Felicetti, B.⁵ Wood, M.⁶ Schonfeld, D.⁷ Mather, O.⁸ Cesura, A.⁹ Barker, J.¹⁰

8
- 70349753296
- R. Percudani, A. Peracchi, BMC Bioinformatics 2009, 10, 273-280.
- (2009) BMC Bioinformatics , vol.10 , pp. 273-280
- Percudani, R.¹ Peracchi, A.²

9
- 85164050549
- B6 DataBase, Home of B6-dependent enzymes, URL http://bioinformatics. unipr.it/B6db.
- B6 DataBase, Home of B6-dependent Enzymes

10
- 0034601688
- J. De Miranda, A. Santoro, S. Engelender, H. Wolosker, Gene 2000, 256, 183-188.
- (2000) Gene , vol.256 , pp. 183-188
- De Miranda, J.¹ Santoro, A.² Engelender, S.³ Wolosker, H.⁴

11
- 2942595866
- M. Xia, Y. Liu, D. J. Figueroa, C. S. Chiu, N. Wei, A. M. Lawlor, P. Lu, C. Sur, K. S. Koblan, T. M. Connolly, Brain Res. 2004, 125, 96-104.
- (2004) Brain Res. , vol.125 , pp. 96-104
- Xia, M.¹ Liu, Y.² Figueroa, D.J.³ Chiu, C.S.⁴ Wei, N.⁵ Lawlor, A.M.⁶ Lu, P.⁷ Sur, C.⁸ Koblan, K.S.⁹ Connolly, T.M.¹⁰

12
- 50549088687
- F. Baumgart, I. Rodriguez-Crespo, FEBS J. 2008, 275, 3538-3545.
- (2008) FEBS J. , vol.275 , pp. 3538-3545
- Baumgart, F.¹ Rodriguez-Crespo, I.²

13
- 25444532514
- K. Strisovsky, J. Jiraskova, A. Mikulova, L. Rulisek, J. Konvalinka, Biochemistry 2005, 44, 13091-13100.
- (2005) Biochemistry , vol.44 , pp. 13091-13100
- Strisovsky, K.¹ Jiraskova, J.² Mikulova, A.³ Rulisek, L.⁴ Konvalinka, J.⁵

14
- 62449236945
- A. K. Mustafa, D. B. van Rossum, R. L. Patterson, D. Maag, J. T. Ehmsen, S. K. Gazi, A. Chkraborty, R. K. Barrow, L. M. Amzel, S. H. Snyder, Proc. Natl. Acad. Sci. USA 2009, 106, 2921-2926.
- (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 2921-2926
- Mustafa, A.K.¹ Van Rossum, D.B.² Patterson, R.L.³ Maag, D.⁴ Ehmsen, J.T.⁵ Gazi, S.K.⁶ Chkraborty, A.⁷ Barrow, R.K.⁸ Amzel, L.M.⁹ Snyder, S.H.¹⁰

15
- 66149118691
- L. Balan, V. N. Foltyn, M. Zehl, E. Dumin, E. Dikopoltsev, K. Knoh, Y. Ohno, A. Kihara, O. N. Jensen, I. S. Radzishevsky, H. Wolosker, Proc. Natl. Acad. Sci. USA 2009, 106, 7589-7594.
- (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 7589-7594
- Balan, L.¹ Foltyn, V.N.² Zehl, M.³ Dumin, E.⁴ Dikopoltsev, E.⁵ Knoh, K.⁶ Ohno, Y.⁷ Kihara, A.⁸ Jensen, O.N.⁹ Radzishevsky, I.S.¹⁰ Wolosker, H.¹¹

16
- 0026714534
- Y. Nagata, Experentia 1992, 48, 753-755.
- (1992) Experentia , vol.48 , pp. 753-755
- Nagata, Y.¹

17
- 0033932747
- S. H. Snyder, P. M. Kim, Neurochem. Res. 2000, 25, 553-560.
- (2000) Neurochem. Res. , vol.25 , pp. 553-560
- Snyder, S.H.¹ Kim, P.M.²

18
- 77952386888
- P. Sikka, R. Walker, R. Cockayne, M. J. A. Wood, P. J. Harrison, P. W. J. Burnet, J. Neurosci. Res. 2010, 88, 1829-1840.
- (2010) J. Neurosci. Res. , vol.88 , pp. 1829-1840
- Sikka, P.¹ Walker, R.² Cockayne, R.³ Wood, M.J.A.⁴ Harrison, P.J.⁵ Burnet, P.W.J.⁶

19
- 9144232858
- K. Hashimoto, T. Fukushima, E. Shimizu, S. Okada, N. Komatsu, N. Okamura, K. Koike, C. Koizumi, K. Imai, M. Iyo, Prog. Neuro- Psychopharmacol. Biol. Psychiatry 2004, 28, 385-388.
- (2004) Prog. Neuro- Psychopharmacol. Biol. Psychiatry , vol.28 , pp. 385-388
- Hashimoto, K.¹ Fukushima, T.² Shimizu, E.³ Okada, S.⁴ Komatsu, N.⁵ Okamura, N.⁶ Koike, K.⁷ Koizumi, C.⁸ Imai, K.⁹ Iyo, M.¹⁰

20
- 58149373550
- R. Inoue, K. Hashimoto, T. Harai, H. Mori, J. Neurosci. 2008, 28, 14486-14491.
- (2008) J. Neurosci. , vol.28 , pp. 14486-14491
- Inoue, R.¹ Hashimoto, K.² Harai, T.³ Mori, H.⁴

21
- 34648825386
- J. Sasabe, T. Chiba, M. Yamada, K. Okamoto, I. Nishimoto, M. Matsuoka, S. Aiso, EMBO J. 2007, 26, 4149-4159.
- (2007) EMBO J. , vol.26 , pp. 4149-4159
- Sasabe, J.¹ Chiba, T.² Yamada, M.³ Okamoto, K.⁴ Nishimoto, I.⁵ Matsuoka, M.⁶ Aiso, S.⁷

22
- 0032403706
- J. H. Krystal, D. C. D'Souza, Biol. Psychiatry 1998, 44, 1075-1076.
- (1998) Biol. Psychiatry , vol.44 , pp. 1075-1076
- Krystal, J.H.¹ D'souza, D.C.²

23
- 68749087296
- V. Labrie, R. Fukumura, A. Rastogi, L. J. Fick, W. Wang, P. C. Boutros, J. L. Kennedy, M. O. Semeralul, F. H. Lee, G. B. Baker, D. D. Belsham, S. W. Barger, Y. Gondo, A. H. C. Wong, J. C. Roder, Hum. Mol. Genet. 2009, 18, 3227-3243.
- (2009) Hum. Mol. Genet. , vol.18 , pp. 3227-3243
- Labrie, V.¹ Fukumura, R.² Rastogi, A.³ Fick, L.J.⁴ Wang, W.⁵ Boutros, P.C.⁶ Kennedy, J.L.⁷ Semeralul, M.O.⁸ Lee, F.H.⁹ Baker, G.B.¹⁰ Belsham, D.D.¹¹ Barger, S.W.¹² Gondo, Y.¹³ Wong, A.H.C.¹⁴ Roder, J.C.¹⁵

24
- 34548689595
- L. Verrall, M. Walker, N. Rawlings, I. Benzel, J. N.C. Kew, P. J. Harrison, P. W. Burnet, Eur. J. Neurosci. 2007, 26, 1657-1669.
- (2007) Eur. J. Neurosci. , vol.26 , pp. 1657-1669
- Verrall, L.¹ Walker, M.² Rawlings, N.³ Benzel, I.⁴ Kew, J.N.C.⁵ Harrison, P.J.⁶ Burnet, P.W.⁷

25
- 75349083874
- A. K. Mustafa, A. S. Ahmad, E. Zeynalov, S. K. Gazi, G. Sikka, J. T. Ehmsen, R. K. Barrow, J. T. Coyle, S. H. Snyder, S. Dorè, J. Neurosci. 2010, 30, 1413-1416.
- (2010) J. Neurosci. , vol.30 , pp. 1413-1416
- Mustafa, A.K.¹ Ahmad, A.S.² Zeynalov, E.³ Gazi, S.K.⁴ Sikka, G.⁵ Ehmsen, J.T.⁶ Barrow, R.K.⁷ Coyle, J.T.⁸ Snyder, S.H.⁹ Dorè, S.¹⁰

26
- 13844294076
- S. D. Dunlop, A. Neidle, Brain Res. 2005, 133, 208-214.
- (2005) Brain Res. , vol.133 , pp. 208-214
- Dunlop, S.D.¹ Neidle, A.²

27
- 70349640053
- H. E. Hoffman, J. Jiraskova, P. Cigler, M. Sanda, J. Schraml, J. Konvalinka, J. Med. Chem. 2009, 52, 6032-6041.
- (2009) J. Med. Chem. , vol.52 , pp. 6032-6041
- Hoffman, H.E.¹ Jiraskova, J.² Cigler, P.³ Sanda, M.⁴ Schraml, J.⁵ Konvalinka, J.⁶

28
- 54849404912
- H. E. Hoffman, J. Jiraskova, M. Ingr, M. Zvelebil, J. Konvalinka, Protein Expression Purif. 2009, 63, 62-67.
- (2009) Protein Expression Purif. , vol.63 , pp. 62-67
- Hoffman, H.E.¹ Jiraskova, J.² Ingr, M.³ Zvelebil, M.⁴ Konvalinka, J.⁵

29
- 70350035997
- M. Goto, T. Yamauchi, N. Kamiya, I. Miyahara, T. Yoshimura, H. Mihara, T. Kurihara, K. Hirotsu, N. Esaki, J. Biol. Chem. 2009, 284, 25944-25952.
- (2009) J. Biol. Chem. , vol.284 , pp. 25944-25952
- Goto, M.¹ Yamauchi, T.² Kamiya, N.³ Miyahara, I.⁴ Yoshimura, T.⁵ Mihara, H.⁶ Kurihara, T.⁷ Hirotsu, K.⁸ Esaki, N.⁹

30
- 67649670256
- T. Yamauchi, M. Goto, H. Y. Wu, T. Uo, T. Yoshimura, H. Mihara, T. Kurihara, I. Miyahara, K. Hirotsu, N. Esaki, J. Biochem. 2009, 145, 421-424.
- (2009) J. Biochem. , vol.145 , pp. 421-424
- Yamauchi, T.¹ Goto, M.² Wu, H.Y.³ Uo, T.⁴ Yoshimura, T.⁵ Mihara, H.⁶ Kurihara, T.⁷ Miyahara, I.⁸ Hirotsu, K.⁹ Esaki, N.¹⁰

31
- 36749083505
- J. A. Hanson, K. Duderstadt, L. P. Watkins, S. Bhattacharyya, J. Brokaw, J. W. Chu, H. Yang, Proc. Natl. Acad. Sci. USA 2007, 46, 18055-18060.
- (2007) Proc. Natl. Acad. Sci. USA , vol.46 , pp. 18055-18060
- Hanson, J.A.¹ Duderstadt, K.² Watkins, L.P.³ Bhattacharyya, S.⁴ Brokaw, J.⁵ Chu, J.W.⁶ Yang, H.⁷

32
- 41949132916
- M. Totrov, R. Abagyan, Curr. Opin. Struct. Biol., 2005, 18, 178-184.
- (2005) Curr. Opin. Struct. Biol. , vol.18 , pp. 178-184
- Totrov, M.¹ Abagyan, R.²

33
- 54549098184
- P. Cozzini, G. E. Kellog, F. Spyrakis, D. J. Abraham, G. Costantino, A. Emerson, F. Fanelli, H. Gohlke, L. A. Kuhn, G. M. Morris, M. Orozco, T. A. Pertinhez, M. Rizzi, C. A. Sottrifer, J. Med. Chem. 2008, 51, 6237-6255.
- (2008) J. Med. Chem. , vol.51 , pp. 6237-6255
- Cozzini, P.¹ Kellog, G.E.² Spyrakis, F.³ Abraham, D.J.⁴ Costantino, G.⁵ Emerson, A.⁶ Fanelli, F.⁷ Gohlke, H.⁸ Kuhn, L.A.⁹ Morris, G.M.¹⁰ Orozco, M.¹¹ Pertinhez, T.A.¹² Rizzi, M.¹³ Sottrifer, C.A.¹⁴

34
- 77951992987
- I. R. Craig, J. W. Essex, K. Spiegel, J. Chem. Inf. Model. 2010, 50, 511-524.
- (2010) J. Chem. Inf. Model. , vol.50 , pp. 511-524
- Craig, I.R.¹ Essex, J.W.² Spiegel, K.³

35
- 0035756145
- K. Soda, T. Yoshimura, N. Esaki, Chem. Record 2001, 1, 373-384.
- (2001) Chem. Record , vol.1 , pp. 373-384
- Soda, K.¹ Yoshimura, T.² Esaki, N.³

36
- 0036303304
- A. I. Denesyuk, K. A. Denessiouk, T. Korpela, M. S. Johnson, J. Mol. Biol. 2002, 316, 155-172.
- (2002) J. Mol. Biol. , vol.316 , pp. 155-172
- Denesyuk, A.I.¹ Denessiouk, K.A.² Korpela, T.³ Johnson, M.S.⁴

37
- 70349087290
- J. P. Richard, T. L. Amyes, J. Crugeiras, A. Rios, Curr. Opin. Chem. Biol. 2009, 13, 475-483.
- (2009) Curr. Opin. Chem. Biol. , vol.13 , pp. 475-483
- Richard, J.P.¹ Amyes, T.L.² Crugeiras, J.³ Rios, A.⁴

38
- 77950481561
- J. Ortega-Castro, M. Adrover, J. Frau, A. Salv à, J. Donoso, F. Munoz, J. Phys. Chem. A 2010, 114, 4634-4640.
- (2010) J. Phys. Chem. A , vol.114 , pp. 4634-4640
- Ortega-Castro, J.¹ Adrover, M.² Frau, J.³ Salvà, A.⁴ Donoso, J.⁵ Munoz, F.⁶

39
- 58249145025
- R. Casanovas, A. Salvà, J. Frau, J. Donoso, F. Munoz, Chem. Phys. 2009, 355, 149-156.
- (2009) Chem. Phys. , vol.355 , pp. 149-156
- Casanovas, R.¹ Salvà, A.² Frau, J.³ Donoso, J.⁴ Munoz, F.⁵

40
- 77953661074
- R. S. Phillips, S. Lima, R. Khristoforov, B. Sudararaju, Biochemistry 2010, 49, 5066-5073.
- (2010) Biochemistry , vol.49 , pp. 5066-5073
- Phillips, R.S.¹ Lima, S.² Khristoforov, R.³ Sudararaju, B.⁴

41
- 23444454552
- D. A. Case, T. E. Cheatham III, T. Darden, H. Gohlke, R. Luo, M. Merz Jr. , A. Onufriev, C. Simmerling, B. Wang, R. Woods, J. Comput. Chem. 2005, 26, 1668-1688.
- (2005) J. Comput. Chem. , vol.26 , pp. 1668-1688
- Case, D.A.¹ Cheatham Iii, T.E.² Darden, T.³ Gohlke, H.⁴ Luo, R.⁵ Merz Jr., M.⁶ Onufriev, A.⁷ Simmerling, C.⁸ Wang, B.⁹ Woods, R.¹⁰

42
- 84875490699
- Amber Home Page
- Assisted Model Building with Energy Refinement, Amber Home Page, URL, http://ambermd.org/.
- Assisted Model Building with Energy Refinement

43
- 0001729674
- G. M. Bradbrook, T. Gleichmann, S. J. Harrop, J. Habash, J. Raftery, J. Kalb, J. Yariv, H. I. Hillier, J. R. Helliwell, J. Chem. Soc. Faraday Trans. 1998, 64, 1603-1611.
- (1998) J. Chem. Soc. Faraday Trans. , vol.64 , pp. 1603-1611
- Bradbrook, G.M.¹ Gleichmann, T.² Harrop, S.J.³ Habash, J.⁴ Raftery, J.⁵ Kalb, J.⁶ Yariv, J.⁷ Hillier, H.I.⁸ Helliwell, J.R.⁹

44
- 85164042388
- Bryce Group
- Bryce Group, Computational Biophysics and Drug Design, URL http://www.pharmacy.manchester.ac.uk/bryce/amber#ion.
- Computational Biophysics and Drug Design

45
- 0029878720
- W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graph. 1996, 14, 33-38.
- (1996) J. Mol. Graph. , vol.14 , pp. 33-38
- Humphrey, W.¹ Dalke, A.² Schulten, K.³

46
- 85164046657
- CINECA, URL http://www.cineca.it

47
- 33846823909
- T. Darden, D. York, L. Pedersen, J. Chem. Phys. 1993, 98, 10089-10092.
- (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
- Darden, T.¹ York, D.² Pedersen, L.³

48
- 85164051347
- Theoretical and Computational Biophysics Group
- Theoretical and Computational Biophysics Group, URL http://www.ks.uiuc. edu/Research/vmd/plugins.

49
- 77956319507
- Schrçdinger, LLC, New York
- Maestro, version 9.0, Schrçdinger, LLC, New York, 2009.
- (2009) Maestro, Version 9.0

50
- 17144385534
- N. Triballeau, F. Acher, I. Brabet, J. P. Pin, H. O. Bertrand, J. Med. Chem. 2005, 48, 2534-2547.
- (2005) J. Med. Chem. , vol.48 , pp. 2534-2547
- Triballeau, N.¹ Acher, F.² Brabet, I.³ Pin, J.P.⁴ Bertrand, H.O.⁵

51
- 41349093326
- A. Nicholls, J. Comput. Aided Mol. Des. 2008, 22, 239-255.
- (2008) J. Comput. Aided Mol. Des. , vol.22 , pp. 239-255
- Nicholls, A.¹

52
- 77953892885
- Y. Gogami, A. Kobayashi, T. Ikeuchi, T. Oikawa, Chem. Biodiversity 2010, 7, 1579-1590.
- (2010) Chem. Biodiversity , vol.7 , pp. 1579-1590
- Gogami, Y.¹ Kobayashi, A.² Ikeuchi, T.³ Oikawa, T.⁴

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.