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Volumn 111, Issue 43, 2007, Pages 12573-12581

QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5′-monophosphate decarboxylase using two different QM regions: Acceleration too small to explain rate of enzyme catalysis

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYLATION; CATALYSIS; COMPUTATIONAL METHODS; MOLECULAR MECHANICS; QUANTUM THEORY;

EID: 36048971666     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp074858n     Document Type: Article
Times cited : (49)

References (73)
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    • Reference deleted in proof.
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    • 84906385292 scopus 로고    scopus 로고
    • For more information on CP2K, see: http://cp2k.berlios.de/.
    • For more information on CP2K, see: http://cp2k.berlios.de/.
  • 40
    • 84906399779 scopus 로고    scopus 로고
    • MacKerell, A. D., Jr.; Brooks, B.; Brooks, C. L., III; Nilsson, L.; Roux, B.; Won, Y.; Karplus M. In The Encyclopedia of Computational Chemistry, 1; Schleyer, P. v. R., et al., Ed.; John Wiley & Sons: Chichester, U.K., 1998; pp 271-277,.
    • MacKerell, A. D., Jr.; Brooks, B.; Brooks, C. L., III; Nilsson, L.; Roux, B.; Won, Y.; Karplus M. In The Encyclopedia of Computational Chemistry, Vol. 1; Schleyer, P. v. R., et al., Ed.; John Wiley & Sons: Chichester, U.K., 1998; pp 271-277,.
  • 48
    • 84906370932 scopus 로고    scopus 로고
    • Frisch, M. J, Trucks, G. W, Schlegel, H. B, Scuseria, G. E, Robb, M. A, Cheeseman, J. R, Montgomery, J. A, Jr, Vreven, T, Kudin, K. N, Burant, J. C, Millam, J. M, Iyengar, S. S, Tomasi, J, Barone, V, Mennucci, B, Cossi, M, Scalmani, G, Rega, N, Petersson, G. A, Nakatsuji, H, Hada, M, Ehara, M, Toyota, K, Fukuda, R, Hasegawa, J, Ishida, M, Nakajima, T, Honda, Y, Kitao, O, Nakai, H, Klene, M, Li, X, Knox, J. E, Hratchian, H. P, Cross, J. B, Bakken, V, Adamo, C, Jaramillo, J, Gomperts, R, Stratmann, R. E, Yazyev, O, Austin, A. J, Cammi, R, Pomelli, C, Ochterski, J. W, Ayala, P. Y, Morokuma, K, Voth, G. A, Salvador, P, Dannenberg, J. J, Zakrzewski, V. G, Dapprich, S, Daniels, A. D, Strain, M. C, Farkas, O, Malick, D. K, Rabuck, A. D, Raghavachari, K, Foresman, J. B, Ortiz, J. V, Cui, Q, Baboul, A. G, Clifford, S, Cioslowski, J, Stefanov, B. B, Liu, G, Liashenko, A, Piskorz, P, Komaromi, I, Martin, R. L, Fox, D. J, Keit
    • Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision D.01; Gaussian, Inc.: Wallingford, CT, 2004.
  • 50
    • 84906385293 scopus 로고    scopus 로고
    • Deleted at proof
    • Deleted at proof.
  • 58
    • 84906370933 scopus 로고    scopus 로고
    • 2 of the amide side chain forms hydrogen bonds with the phosphate group and O2 of BMP. The reference for the crystal structure (ref 13) describes a hydrogen bond between Gln215 and BMP at O2. It is likely there is a mistake in the PDB file, and the positions of the N and O of the amide should be reversed.
    • 2 of the amide side chain forms hydrogen bonds with the phosphate group and O2 of BMP. The reference for the crystal structure (ref 13) describes a hydrogen bond between Gln215 and BMP at O2. It is likely there is a mistake in the PDB file, and the positions of the N and O of the amide should be reversed.
  • 59
    • 84906414176 scopus 로고    scopus 로고
    • The heavy atom distances are 3.76 and 2.66 Å in the crystal structure and simulation, respectively.
    • The heavy atom distances are 3.76 and 2.66 Å in the crystal structure and simulation, respectively.
  • 60
    • 84906385287 scopus 로고    scopus 로고
    • The heavy atom distances are 2.76 and 4.20 Å in the crystal structure and simulation, respectively.
    • The heavy atom distances are 2.76 and 4.20 Å in the crystal structure and simulation, respectively.
  • 61
    • 84906385288 scopus 로고    scopus 로고
    • The heavy atom distances are 3.17 and 5.74 Å in the crystal structure and simulation, respectively.
    • The heavy atom distances are 3.17 and 5.74 Å in the crystal structure and simulation, respectively.
  • 63
    • 84906385289 scopus 로고    scopus 로고
    • The heavy atom distances are 2.92 and 3.20 Å in the large and small QM TS structures, respectively.
    • The heavy atom distances are 2.92 and 3.20 Å in the large and small QM TS structures, respectively.
  • 65
    • 84906414177 scopus 로고    scopus 로고
    • uncat.
    • uncat.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.