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Volumn 111, Issue 7, 2007, Pages 1823-1833

Three-dimensional structure and dynamics of a de novo designed, amphiphilic, metallo-porphyrin-binding protein maquette at soft interfaces by molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPUTER SIMULATION; MOLECULAR STRUCTURE; PEPTIDES; PROTEINS;

EID: 33847718675     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0666378     Document Type: Article
Times cited : (16)

References (38)
  • 21
    • 84906384980 scopus 로고    scopus 로고
    • MD simulation results indicate that the rmsd of the backbone atoms of the equilibrated structure compared to that of the crystal structure is 0.80 ± 0.09 Å. The average interhelix separation is ∼10.8 Å from the simulation result compared to ∼10.7 Å from the crystal structure
    • MD simulation results indicate that the rmsd of the backbone atoms of the equilibrated structure compared to that of the crystal structure is 0.80 ± 0.09 Å. The average interhelix separation is ∼10.8 Å from the simulation result compared to ∼10.7 Å from the crystal structure.
  • 35
    • 84906413587 scopus 로고    scopus 로고
    • The concept of crossing angle was borrowed from ref 31. For an idealized model of two short sections of a-helix, it is defined as the angle between the axes of the two helices. Our definition of crossing angles is the angle between the principal axes (i.e, using the coordinate axis of the principal moment of inertia) of two neighboring helices. This definition is an approximation, and it could be too coarse to be meaningful for coiled coils with several turns of the major helix or for substantially distorted helices such as the case for holo-AP0. However, first, the bundles in our case are short around one-third of the pitch of the major helix, so the assumption that the long principal axis of the helix is approximately the axis of the helix is acceptable. Second, our calculation of the crossing angle for the helices of holo-AP0 is only for comparison with that of the apo-form and to thereby show that the holo-form is not a coiled coil
    • The concept of crossing angle was borrowed from ref 31. For an idealized model of two short sections of a-helix, it is defined as the angle between the axes of the two helices. Our definition of crossing angles is the angle between the principal axes (i.e., using the coordinate axis of the principal moment of inertia) of two neighboring helices. This definition is an approximation, and it could be too coarse to be meaningful for coiled coils with several turns of the major helix or for substantially distorted helices such as the case for holo-AP0. However, first, the bundles in our case are short (around one-third of the pitch of the major helix), so the assumption that the long principal axis of the helix is approximately the axis of the helix is acceptable. Second, our calculation of the crossing angle for the helices of holo-AP0 is only for comparison with that of the apo-form and to thereby show that the holo-form is not a coiled coil.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.