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Volumn 111, Issue 15, 2007, Pages 3969-3976

Calculation of redox properties: Understanding short- and long-range effects in rubredoxin

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; DENSITY FUNCTIONAL THEORY; ELECTRONIC STRUCTURE; PROTEINS;

EID: 34247868775     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp067387y     Document Type: Article
Times cited : (88)

References (63)
  • 1
    • 2142807131 scopus 로고    scopus 로고
    • Huber, R, Wieghardt, K, Poulos, T, Eds, Wiley: New York, and references therein
    • Meyer J.; Moulis J. M. Rubredoxin. In Handbook of Metalloproteins; Messerschmidt, A,. Huber, R., Wieghardt, K., Poulos, T., Eds.; Wiley: New York,2001; pp 505-517 and references therein.
    • (2001) Handbook of Metalloproteins; Messerschmidt, A , pp. 505-517
    • Meyer, J.1    Rubredoxin, M.J.M.2
  • 24
    • 15344345714 scopus 로고    scopus 로고
    • The CP2K developers group, 2005: http://cp2k.berlios.de/. Vande-Vondele, J.; Krack, M.; Mohamed, F.; Parrinello, M.; Chassaing, T.; Hutter, J. Comput. Phys. Commun. 2005, 167, 103-128.
    • The CP2K developers group, 2005: http://cp2k.berlios.de/. Vande-Vondele, J.; Krack, M.; Mohamed, F.; Parrinello, M.; Chassaing, T.; Hutter, J. Comput. Phys. Commun. 2005, 167, 103-128.
  • 29
    • 84906389210 scopus 로고    scopus 로고
    • The bias created by averaging over configurations generated by a Hamiltonion deviating from the true Hamiltonian can be eliminated by including a weight factor consisting of the Boltzmann exponent of the difference in energy of the target Hamiltonian and sampling Hamiltonian.4 However, for our system, these energy differences are dominated by errors in the DFT description of the intermolecular interactions stabilizing the protein structure. The classical force field model, which has been designed for this purpose, is in fact much more reliable. Correcting for the difference between the DFT and classical model would therefore deteriorate rather than improve the accuracy of our results for the redox properties, which is why we have not applied such a procedure
    • 4 However, for our system, these energy differences are dominated by errors in the DFT description of the intermolecular interactions stabilizing the protein structure. The classical force field model, which has been designed for this purpose, is in fact much more reliable. Correcting for the difference between the DFT and classical model would therefore deteriorate rather than improve the accuracy of our results for the redox properties, which is why we have not applied such a procedure.
  • 39
    • 84906389211 scopus 로고    scopus 로고
    • The high spin multiplicity for the system discussed here might raise questions about the validity of our approximation to the exchange and correlation functional BLYP, However, in our case both oxidized and reduced states have high multiplicity. Vacuum calculations for similar systems indicate that DFT can give quite good results in contrast to, for example, haemes, where high and low spin states are compared
    • The high spin multiplicity for the system discussed here might raise questions about the validity of our approximation to the exchange and correlation functional (BLYP). However, in our case both oxidized and reduced states have high multiplicity. Vacuum calculations for similar systems indicate that DFT can give quite good results in contrast to, for example, haemes, where high and low spin states are compared.
  • 52
    • 84906403680 scopus 로고    scopus 로고
    • Counterions contribute very little to the total reorganization energy (10% for CpRd and 6% for PfRd). Over the sampled time scale of 5 ns, none of them was seen to approach the metal center closer than 7 Å, which could perturb the metal coordination properties.
    • Counterions contribute very little to the total reorganization energy (10% for CpRd and 6% for PfRd). Over the sampled time scale of 5 ns, none of them was seen to approach the metal center closer than 7 Å, which could perturb the metal coordination properties.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.