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Volumn 286, Issue 5444, 1999, Pages 1579-1583

Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR

Author keywords

[No Author keywords available]

Indexed keywords

CELL RECEPTOR; VIRUS RECEPTOR;

EID: 0033584785     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.286.5444.1579     Document Type: Article
Times cited : (385)

References (32)
  • 4
    • 13044294136 scopus 로고    scopus 로고
    • note
    • 2-terminal fragment (residues 22 to 125) of the cellular receptor (CAR D1) were expressed in E. coli and purified as described previously (3). Purified proteins were proteolysed separately with trypsin (10 mg/ml). The 1:3 (trimeric knob: CAR D1) complex was formed at room temperature and purified by anion exchange chromatography. Crystals of Ad12 knob were grown at room temperature with the sitting drop vapor diffusion method from an Ad12 knob solution of 20 mg/ml suspended over a reservoir of 26% polyethylene glycol (PEG) 3350. Showers of small, poorly ordered crystals grew over the course of a week and were used to seed a 10-μl drop containing equal volumes of Ad12 knob and 26% PEG 3350 over a reservoir of 26% PEG 3350. Typically, crystals grew overnight as rhombohedral plates (0.5 mm by 0.5 mm by 0.2 mm). They were flash cooled at 99 K with 50% PEG 3350 as a cryoprotectant. Crystals of the complex were grown at room temperature with the sitting drop vapor diffusion method from 0.9 M ammonium sulfate in 100 mM MES (pH 6.2). Mercury was introduced into the Ad12 knob-CAR D1 complex by soaking a single CAR D1-knob complex crystal in 10 mM thimerosal for 6 hours. Crystals were flash cooled at 99 K, with 50% ethylene glycol as a cryoprotectant Data were processed with the HKL Program Suite (22). The structure of Ad12 knob was solved by molecular replacement (23), with a monomer of Ad5 knob [Protein Data Bank (PDB) accession number 1KNB.PDB] as a search model Six monomers were placed and their positions were refined with rigid body refinement. Simulated annealing protocols in CNS (24) with the use of tight NCS restraints were punctuated by rounds of model building. The refinement statistics are shown in Table 1. The structure of the Ad12 knob-CAR D1 complex was determined with a combination of single isomorphous replacement (SIR), solvent flattening, and molecular replacement. The refined structure of the Ad12 knob monomer was used as a search model in molecular replacement. A single, clear solution was found corresponding to a monomer in the asymmetric unit such that the biological three-fold axis was coincident with the cristallographic axis. The heavy atom position was determined by visual inspection of a difference map with model phases, and its position was refined with MLPHARE (23). Phase combination with the use of the Ad12 knob structure and the experimental SIR phases followed by solvent flattening with the program DM (23) resulted in a map with a mean figure of merit (FOM) of 0.74. The structure was refined with CNS punctuated by rounds of model building.
  • 6
    • 13044306092 scopus 로고    scopus 로고
    • note
    • Ad12 knob is 48% identical and 78% similar in sequence to Ad5 knob, which also binds CAR. The structures are essentially identical and have a root mean square deviation of 1.2 A when equivalent Ca atoms are superimposed.
  • 9
    • 13044250562 scopus 로고    scopus 로고
    • note
    • On the basis of an search of the DALI database (25), the structure of CAR D1 most closely resembles the structures of (in descending order) the extracellular domain of the myelin adhesion molecule (26), domain 1 of human CD4 (27), a receptor for HIV, and several other cell surface glycoproteins. Although all of these molecules share a common fold, large differences in strand lengths and loop conformations are evident when equivalent atoms are superimposed.
  • 10
    • 13044256495 scopus 로고    scopus 로고
    • note
    • Domain 1 of CD4 (1cdh.pdb), ICAM-1 (1iam.pdb and lic1.pdb), and ICAM2 (1zxq.pdb) (where the names of the molecules are followed by their PDB access identification numbers) were superimposed on the structure of CAR D1. The positions of the second domain were used to infer a possible position of CAR D2.
  • 11
    • 13044304653 scopus 로고    scopus 로고
    • note
    • Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H. His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg S, Ser; T. Thr; V, Val; W, Trp; and Y, Tyr.
  • 14
    • 13044294135 scopus 로고    scopus 로고
    • note
    • All Ad12 knob variants listed were constructed by primer-directed PCR mutagenesis and confirmed by nucleotide sequence analysis. The knob variants were purified as previously described for native Ad12 knob. A filter-binding assay was used as an initial screen for the effects of substitutions in knob on CAR D1 binding. Purified variant or wild-type His-tagged knob proteins were briefly immobilized on nitrocellulose membranes (5 μg per dot) and fixed with 0.25% glutaraldehyde in phosphate-buffered saline (PBS). The membranes were probed with biotinytated CAR D1 (5 mg/ml), and bound CAR D1 was visualized with 1:500 horseradish peroxidase (HRP)-conjugated mouse monoclonal antibody to biotin (Sigma) with the use of a chemiluminescent substrate (SuperSignal, Pierce, Rockford, IL). A duplicate membrane was used to quantitate bound protein with rabbit antiserum to Ad12 knob followed by HRP goat antibody to rabbit IgG (Cappel, Cochranville, PA) and chemiluminescent detection. All assays were performed in duplicate. Two other methods were used to confirm results and provide a more quantitative estimate for the effect of these substitutions. First, CAR D1 binding by knob variants were characterized by size exclusion chromatography (SEC) or a TSK G3000 SWXL (7.8 mm by 30 cm) column. The extent of complex formation in 25 mM MES (pH 6.5) and 200 mN NaCl was estimated from the changes in elution volume of the complex. Under these conditions, wild-type complex is well resolved from free CAR D1 and Ad 12 knob (3). Second, we examined complex formation with a native polyacrylamide gel electrophoresis gel assay. Complexes farmed at varying ratios of CAR 01 to Ad12 knob or its variants were electrophoresed on a 7% native gel. Under these conditions, free knob barely enters the gel, and the complex migrates between free knob and free CAR D1.
  • 15
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    • Supplemental data available at www.sciencemag.org/ feature/data/1043056.shl.
  • 16
    • 13044264562 scopus 로고    scopus 로고
    • note
    • Surface accessible areas were determined by the method of Lee and Richards (28) with the program ACCESS with a probe radius of 1.4 Å.
  • 21
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    • P. D. Kwong et al., Nature 393, 648 (1998).
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    • R. Wyatt et al., Nature 393, 705 (1998).
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    • Wyatt, R.1
  • 23
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    • C. W. Carter and R. M. Sweet, Eds. Academic Press, New York
    • Z. Otwinowski and W. Minor, in Methods in Enzymology, vol. 276, C. W. Carter and R. M. Sweet, Eds. (Academic Press, New York, 1997), pp. 307-326.
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    • Otwinowski, Z.1    Minor, W.2
  • 32
    • 13044249253 scopus 로고    scopus 로고
    • note
    • The authors thank V. Graziano for analyzing the binding affinities of the knob variants; M. Rossmann, D. Engelman, C. Anderson, J. Dunn, and J. Kuryian for critically reading the manuscript and suggesting improvements; and L. Berman, R. Sweet, and J. Berendsen for access to beamlines X25, X12C, and X8C, respectively. This research was supported by NIH grant AI362S1 to P.F. and by the Office of Biological and Environmental Research of the U.S. Department of Energy under Prime Contract DE-AC02-98CH10886 with Brookhaven National Laboratory. The macromolecular crystallography beamlines X25, X12C, and X8C, at the National Synchrotron Light Source, are also supported by NSF and by NIH grant 1P41 RR12408-01A1. Coordinates have been deposited in the Protein Data Bank with accession codes 1NOB and 1KAC for Ad12 knob and Ad12 knob in complex with CAR D1, respectively.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.