Appeal 2007-2956
Application 10/677,733
provided to explain why it is reasonable for skilled persons in the art to
believe that the prior art PAS domain proteins possesses the claimed
limitation of “the PAS domain is predetermined, prefolded in its native state,
and comprises a hydrophobic core that has no NMR-apparent a priori
formed ligand cavity.” Thus, there is sufficient evidence to shift the burden
to Appellants to show that the claimed subject matter does not possesses the
recited limitation.
Appellants contend that
the prior work provided no evidence of cofactors for most PAS
domains, and taught that those limited PAS domains having
cofactors required them for proper folding, and taught that PAS
domains without cofactors had tightly packed cores with no
pre-formed cavities that would suggest a cofactor or ligand
binding site, one skilled in the art would not have suspected that
such PAS domains (without known cofactors and having tightly
packed cores with no pre-formed cavities that would suggest a
cofactor or ligand binding site) would be rational candidates to
screen for core ligand binding; in fact, the art (supra) teaches
squarely away from such use.
(App. Br. 5.)
We do not agree that “one skilled in the art would not have suspected
that . . . PAS domains (without known cofactors and having tightly packed
cores with no pre-formed cavities that would suggest a cofactor or ligand
binding site) would be rational candidates to screen for core ligand binding”
(Appeal Br. 5). Takahaski suggests a method for identifying ligands for a
PAS protein having a hydrophobic core (Answer 6). Edery also describes an
assay method for identifying compounds that regulate a PAS domain
protein’s activity. Thus, despite the fact that these proteins have tightly
packed cores with no pre-formed cavities – a fact that Appellants have not
challenged – it was still suggested that these PAS domain proteins be
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