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Volumn 121, Issue 5, 2004, Pages 2412-2421

Interplay of secondary structures and side-chain contacts in the denatured state of BBA1

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMIC SIMULATIONS; HYDROPHOBIC CONTACTS; PROTEIN DENATURATION; SALT BRIDGES; SOLVATION;

EID: 4043074044     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1768151     Document Type: Article
Times cited : (19)

References (96)
  • 31
    • 4043184400 scopus 로고    scopus 로고
    • note
    • Ab initio protein folding simulations, with the aim to reach the native state under the native condition, are far more challenging due to the constraints of reproducing folding time scales (thus folding reaction cannot be artificially accelerated) and reproducing time-dependent folding events (thus dynamics trajectories cannot be interrupted as in the multicanonical methods, Ref. 24). There are only a handful of ab initio folding simulations reported in the literature, including the works on an all a protein, villin headpiece (Refs. 50 and 91), and several α-β proteins such as Trp-cage and BBA5 (Refs. 44, 49, and 92-94), These simulations use various approximations and are still very limited.
  • 51
    • 4043117963 scopus 로고    scopus 로고
    • E. Z. Wen and R. Luo, (unpublished)
    • E. Z. Wen and R. Luo, (unpublished).
  • 53
    • 4043180132 scopus 로고    scopus 로고
    • M. J. Hsieh and R. Luo, Proteins (to be published)
    • M. J. Hsieh and R. Luo, Proteins (to be published).
  • 59
  • 62
    • 4043137582 scopus 로고    scopus 로고
    • T. Z. Lwin, Q. Lu, R. H. Zhou, and R. Luo (unpublished)
    • T. Z. Lwin, Q. Lu, R. H. Zhou, and R. Luo (unpublished).
  • 68
    • 4043062499 scopus 로고    scopus 로고
    • note
    • The simulated time scales are at least 200 shorter the physical time scales due to the enhanced sampling method (about a factor of 20, Ref. 55) and the use of no friction (at least a factor of 10, Ref. 95) in implicit solvation.
  • 71
    • 4043080896 scopus 로고    scopus 로고
    • note
    • One cause for such a low percentage of β hairpin is due to the rather stringent standard used for β-hairpin definition: when applied to the 35 frames in the NMR structure of BBA1, the β hairpin can only be observed once. The NMR structures at residues 2-7 are mostly classified as strand (S) or nonstructured.
  • 73
    • 4043061085 scopus 로고    scopus 로고
    • note
    • Statistical dependence of the native hairpin upon the native helix is difficult to obtain because the native hairpin population is too low to make a quantitative conclusion.
  • 77
    • 4043095128 scopus 로고    scopus 로고
    • note
    • It should be pointed out that local protein environments strongly influence the strength of a salt bridge. It is possible that a salt bridge is highly unfavorable, for example, in a buried environment due to desolvation. With the much confined set of solvent-exposed salt bridges, a counterexample still exists: addition of oppositely charged groups in T4 lysozyme in solvent-exposed positions that might permit them to form, salt bridges led to little if any net stabilization of the native state (Ref. 96). The seemingly contradictory claims are in part due to the fact that they do not express the energy of a salt bridge relative to the same reference state. In computational studies, salt bridges are broken not by deleting the charged groups from the protein, but by moving the charged groups away from each other. However in the experimental study, salt bridges are broken by deleting one or both charged groups. This results in a very different reference state, because adding charged groups to certain sites on a protein can be intrinsically destabilizing, as observed in the same T4 lysozyme study (Ref. 9.6). This issue has been discussed previously (Refs. 78 and 80).
  • 82
    • 4043051195 scopus 로고    scopus 로고
    • note
    • Both hydrophobic and salt-bridge populations are generally higher in the native state when preorganized backbone restricts side-chain motions involved in such interactions.
  • 84
    • 4043129213 scopus 로고    scopus 로고
    • note
    • This is the average simulation time interval separating the occurrences of the full native helix.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.