Appeal No. 2000-0137 Page 9
Application No.08/646,558
of the specification and without reading that limitation out of the claims? Let’s
review the evidence:
• the claims themselves suggest that “aromatic or hydrophobic” amino
acids include Arg, Lys, Gly and Cys;
• the specification suggests that hydrophobic amino acids include Lys,
Cys, Tyr, Asp, Leu, Ile, Val, Met, Trp, and Phe;
• the Appeal Brief argues that the hydrophobic amino acids are Val, Leu,
Ile, Phe, Trp, Tyr, Cys, and Met, and do not include Gly, Arg, or Ala;
• the text cited by Appellants states that the aromatic amino acids are
Phe, Trp, and Tyr, and that the hydrophobic amino acids include Val, Leu, and Ile
but not Gly, Ala, or Pro; and
• another textbook states that the hydrophobic amino acids are Ala, Val,
Leu, Ile, Pro, Met, Phe, and Trp, and do not include Tyr, Gly, Cys, Asp, Lys or
Arg.
Thus, the specification includes as preferred hydrophobic amino acids
Leu, Ile, Val, Met, Trp, and Phe, all of which are recognized in the art as
hydrophobic. See Lehninger, page 101. However, the specification also
includes as preferred “hydrophobic” amino acids Lys and Asp (which are
positively and negatively charged, respectively, at pH 7) and Cys and Tyr, which
are classified by Lehninger as polar (i.e., hydrophilic).
It is unclear what criteria Appellants are applying in classifying Lys, Asp,
Cys, and Tyr as hydrophobic amino acids. Tyr carries a hydroxyl group on its
side chain, Cys carries a thiol group, and Lys and Asp carry charged reactive
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