Structural basis of amino acid α helix propensity

Science

Volumn 260, Issue 5114, 1993, Pages 1637-1640

  Blaber, Michael ^a   Zhang, Xue Jun ^a   Matthews, Brian W ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

AMINO ACID SUBSTITUTION; ARTICLE; PRIORITY JOURNAL; PROTEIN STRUCTURE;

AMINO ACIDS; BACTERIOPHAGE T4; ENZYME STABILITY; MODELS, MOLECULAR; MURAMIDASE; MUTATION; PROTEIN STRUCTURE, SECONDARY; SUPPORT, NON-U.S. GOV'T; SUPPORT, U.S. GOV'T, P.H.S.; THERMODYNAMICS;

EID: 0027236794     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.8503008     Document Type: Article

References (45)

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12. 44 is included is Leu-Asn-Ala-Ala-Lys-Ser-Glu-Leu-Asp-Lys-Ala-Ile. For the 12 residues in the α helix, the mean Ramachandran angles are φ = -67° ± 9° and ψ = -41° ± 6°.
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18. 1, a = 54.1 Å, b = 55.9 Å, c = 59.9 Å, β = 103.6°, two molecules per asymmetric unit resolution of 1.85 Å; Trp: space group P1, a = 54.4 Å, b = 64.3 Å, c = 59.5 Å, α = 101.1°, β = 89.9°, γ = 115.0°, four molecules per asymmetric unit, resolution of 2.05 Å). All other variants that were crystallized were isomorphous with the wild type (resolution of 1.7 to 1.9 Å). The Glu variant gave crystals in yet another form. Diffraction data were collected (26) and all the structures were determined and refined to the resolution limits defined above (R values between 14.9 and 17.2%; bond length deviation of 0.012 to 0.019 Å; bond angle deviation of 1.9° to 2.3°).
19. 1 = -76°) substitutions at site 131 that β branched amino acids might be helix-destabilizing because of the strain introduced, although the apparent strain energy was not large (17). The possible involvement of strain in such cases remains an open question.
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31. 44, the hydrocarbon surface area that these two residues would then bury is close to their observed hydro-phobic stabilization (→ in fig. 2).
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41. γ of Met) was included in the calculation. The radius of the probe used for the calculations was 1.4 Å. The straight line was fitted by linear regression to the points for Asn, Glu, Ser, Thr, Val, Lys. Ile. and Leu (correlation coefficient = 0.96).
42. -1). Estimates of buried surface area are therefore sensitive to changes in side chain conformation, geometry of the α helix, and the model used in the estimation of the solvent-exposed area in the unfolded state. In an attempt to minimize these sources of uncertainly, we based the surface area calculation only on the side chains of the substituted residue. Calculations of surface area based on the helix as a whole, as well as attempts to estimate entropic effects, will be described elsewhere (M. Blaber et al., in preparation).
43. Abbreviations: A, Ala; C, Cys; D, Asp; E, Glu, F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; Q, Gin; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; Y, Tyr.
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45. We thank S. Pepiot and J. Wozniak for help with purifying the mutant lysozymes, G. D. Rose and F. M. Richards for helpful comments on the manuscript, and J. Lindstrom and W. A. Baase for determining the thermodynamic parameters. Supported by grants from the National Institutes of Health (GM 21967) and the Lucille P. Markey Charitable Trust.