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Volumn 131, Issue 33, 2009, Pages 11825-11832

Breathing motions of a respiratory protein revealed by molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE ROUTES; BIOLOGICAL FUNCTIONS; BREATHING MOTIONS; DISTAL POCKET; DISTAL REGIONS; DYNAMICAL BEHAVIORS; INTERNAL CAVITIES; INTRINSIC FEATURES; MOLECULAR DYNAMICS SIMULATIONS; PROTEIN MATRIX; STATISTICAL APPROACH;

EID: 69049084556     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja9028473     Document Type: Article
Times cited : (28)

References (71)
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    • (2005) Biophys. J , vol.89 , pp. 465-474
    • Bossa, C.1
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    • Agmon, N. Biophys. J. 2004, 87, 1537-1543.
    • (2004) Biophys. J , vol.87 , pp. 1537-1543
    • Agmon, N.1
  • 39
    • 69049107195 scopus 로고    scopus 로고
    • Giammona, D. A. Ph. D. Thesis, University of California, Davis, CA, 1984.
    • Giammona, D. A. Ph. D. Thesis, University of California, Davis, CA, 1984.
  • 44
    • 69049109503 scopus 로고    scopus 로고
    • Uppsala Software Factory. VOIDOO. http://xray.bmc.uu.se/usf/ voidoo.html (accessed July 29, 2009).
    • Uppsala Software Factory. VOIDOO. http://xray.bmc.uu.se/usf/ voidoo.html (accessed July 29, 2009).
  • 45
    • 69049100780 scopus 로고    scopus 로고
    • Quantitative comparison of the gate areas and free-energy profile of a ligand moving inside the protein is not trivial. However, the trend of the average gate areas is in fair agreement with the activation free energies of CO migration inside horse-heart myoglobin obtained by Kato and co-workers 34 e.g, the smaller the gate area, the larger the activation free energy, and vice versa
    • 34 (e.g., the smaller the gate area, the larger the activation free energy, and vice versa).
  • 51
    • 69049119949 scopus 로고    scopus 로고
    • It is worth mentioning that the distribution of all the studied cavities was found to be asymmetric, with a longer tail on the high-side. It was found that a log-normal distribution gave the best to fit these data (better than Gaussian-like functions, Indeed, previous studies have strongly suggested that such behavior is often adopted in nature see, for instance, ref 52
    • It is worth mentioning that the volume distribution of all the studied cavities was found to be asymmetric, with a longer tail on the high-volume side. It was found that a log-normal distribution gave the best to fit these data (better than Gaussian-like functions). Indeed, previous studies have strongly suggested that such behavior is often adopted in nature (see, for instance, ref 52).
  • 54
    • 69049084204 scopus 로고    scopus 로고
    • Though it is beyond the focus of this work, we will briefly mention that 135L regulates the gate between Xe2 and cavity 4, close to the phantom cavities previously observed. This is consistent with previous theoretical studies of ligand migration from the proximal region to the phantom region via a bottleneck close to Xe2 see, for instance, refs 23 and 31
    • Though it is beyond the focus of this work, we will briefly mention that 135L regulates the gate between Xe2 and cavity 4, close to the phantom cavities previously observed. This is consistent with previous theoretical studies of ligand migration from the proximal region to the phantom region via a bottleneck close to Xe2 (see, for instance, refs 23 and 31).
  • 64
  • 65
    • 69049110618 scopus 로고    scopus 로고
    • We cannot exclude the possibility that this result was obtained because our model is based on a met-myoglobin. The water molecule bound to the iron center of the heme group may influence the histidine gate
    • We cannot exclude the possibility that this result was obtained because our model is based on a met-myoglobin. The water molecule bound to the iron center of the heme group may influence the histidine gate.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.