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  • Key words: Hydrophobic interactions  (1)
  • Protein fold recognition  (1)
  • computer-aided molecular modeling  (1)
  • 1
    Electronic Resource
    Electronic Resource
    A new “hydrophobic template” method detects segments forming transmembrane α-helical bundles in ion channels (1999)
    Springer
    Theoretical chemistry accounts 101 (1999), S. 73-76 
    Details
    ISSN: 1432-2234
    Keywords: Key words: Hydrophobic interactions ; Molecular modeling ; Molecular hydrophobicity potential ; Helix-helix contacts ; Protein fold recognition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. We present a “hydrophobic template” method enabling recognition of α-helix bundles in membrane channels from sequence analysis. Inspection of hydrophobic properties of pore-forming helices in proteins with known structure (A-B5 toxins) permits delineation of a common polarity motif: two hydrophobic surface stretches separated by polar areas. The bundles are stabilized by nonpolar interhelical contacts. A number of transmembrane segments were checked for presence of this motif, and it was detected for pore-forming helices of several ion transporters (segments M2 of acetylcholine and GABAA receptors, α5 peptide of δ-endotoxin), which reveal five α-helix bundle architecture. Applications of the method to modeling of membrane channels are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002140050409
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Application of three-dimensional molecular hydrophobicity potential to the analysis of spatial organization of membrane domains in proteins: I. Hydrophobic properties of transmembrane segments of Na+, K+-ATPase (1992)
    Springer
    The protein journal 11 (1992), S. 665-675 
    Details
    ISSN: 1573-4943
    Keywords: Hydrophobicity potential ; membrane domain ; transmembrane helices ; computer-aided molecular modeling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A new computer-aided molecular modeling approach based on the concept of three-dimensional (3D) molecular hydrophobicity potential has been developed to calculate the spatial organization of intramembrane domains in proteins. The method has been tested by calculating the arrangement of membrane-spanning segments in the photoreaction center ofRhodopseudomonas viridis and comparing the results obtained with those derived from the X-ray data. We have applied this computational procedure to the analysis of interhelical packing in membrane moiety of Na+, K+-ATPase. The work consists of three parts. In Part I, 3D distributions of electrostatic and molecular hydrophobicity potentials on the surfaces of transmembrane helical peptides were computed and visualized. The hydrophobic and electrostatic properties of helices are discussed from the point of view of their possible arrangement within the protein molecule. Interlocation of helical segments connected with short extramembrane loops found by means of optimization of their hydrophobic/hydrophilic contacts is considered in Part II. The most probable 3D model of packing of helical peptides in the membrane domain of Na+, K+-ATPase is discussed in the final part of the work.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01024968
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    Paper (German National Licenses)
    Fulltext
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