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Volumn 309, Issue 5742, 2005, Pages 1868-1871

Biochemistry: Toward high-resolution de novo structure prediction for small proteins

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; MOLECULAR BIOLOGY; PROTEINS; SAMPLING;

EID: 24944493938     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1113801     Document Type: Article
Times cited : (737)

References (23)
  • 4
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    • B. Kuhlman et al., Science 302, 1364 (2003).
    • (2003) Science , vol.302 , pp. 1364
    • Kuhlman, B.1
  • 5
    • 0038008976 scopus 로고    scopus 로고
    • J. Tsai et al., Proteins 53, 76 (2003).
    • (2003) Proteins , vol.53 , pp. 76
    • Tsai, J.1
  • 10
    • 24944495696 scopus 로고    scopus 로고
    • note
    • Materials and methods are available as supporting material on Science Online.
  • 11
    • 24944518659 scopus 로고    scopus 로고
    • note
    • Inspection of the multiple sequence alignment revealed that the target sequence had several hydrophobic residues at exposed beta-sheet positions in this topology that were replaced by polar residues in other members of the alignment, which offers a possible explanation for the absence of this topology in target-sequence models.
  • 13
    • 24944525138 scopus 로고    scopus 로고
    • note
    • The single case where non-native models had lower energies than the native is a domain of a larger protein that has a quite hydrophobic interface and may not be stable in isolation.
  • 17
    • 24944590616 scopus 로고    scopus 로고
    • note
    • The physical chemistry of the packing of nonpolar atoms is considerably easier to model than the subtle trade-offs between desolvation of polar groups and the formation of buried polar interactions. Accurate modeling of functional sites may further require inclusion of explicit solvent molecules, modeling of protonation states and interactions with ligands, and polarizible electrostatics treatments. Together with the increase in the cost of refinement with chain length, this has implications for structural genomics efforts: The refinement to high resolution of comparative models of large proteins (>400 amino acids) based on ∼30% sequence identity, with many buried polar and charged residues, may be a harder problem than the de novo prediction of the structures of small proteins.
  • 20
    • 24944454435 scopus 로고    scopus 로고
    • note
    • To conserve computational resources, no round 2 modeling was done for Glucose Permease IIBC because the native topology was never sampled during fragment assembly. Secondary structure predictions for all 50 homologs predicted an alpha helix in place of the N-terminal beta strand in the native structure.
  • 21
    • 24944455289 scopus 로고    scopus 로고
    • note
    • Core residues are defined as those with <20% solvent-accessible surface area compared with an extended G-X-G peptide.
  • 22
    • 24944473308 scopus 로고    scopus 로고
    • DeLano Scientific, San Carlos, CA, USA
    • W. L. Delano (DeLano Scientific, San Carlos, CA, USA, 2002).
    • (2002)
    • Delano, W.L.1
  • 23
    • 24944520961 scopus 로고    scopus 로고
    • note
    • We thank L. Malmström for computational assistance and K. Laidig for flawless administration of the computing resources necessary for these calculations. We gratefully acknowledge support from the Howard Hughes Medical Institute (P.B. and D.B.) and the Helen Hay Whitney Foundation (K.M.S.M.).


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.