Opinion ID: 2653549
Heading Depth: 4
Heading Rank: 1

Heading: The Patentees’ Definition of KARI

Text: The patents provide definitions of several terms, noting that “[t]he following definitions and abbreviations are to be used for the interpretation of the claims and specification.” ’188 Patent col. 7 ll. 12–14. 1 As described above, the patents subsequently define KARI as: 1 Because the specifications of the patents-in-suit largely are identical, the court for brevity will cite only to the ’188 patent. BUTAMAX(TM) ADVANCED BIOFUELS v. GEVO, INC. 13 an enzyme that catalyzes the conversion of aceto- lactate to 2,3-dihydroxyisovalerate using NADPH (reduced nicotinamide adenine dinucleotide phosphate) as an electron donor. Preferred acetohy- droxy acid isomeroreductases are known by the EC number 1.1.1.86 and sequences are available from a vast array of microorganisms, including but not limited to . . . Methanococcus maripalu- dis . . . . ’188 Patent col. 7 ll. 35–47. It cannot be disputed that the patentees offered a definition of KARI. It is disputed, however, whether this definition “clearly expresses an intent” to redefine KARI in a way that differs from the plain and ordinary meaning identified above and, if so, the extent of any such difference. Gevo contends that the phrase “using NADPH . . . as an electron donor” is a clear expression of the patentees’ intent to exclude KARI that are not “NADPH- dependent.” Butamax disagrees and asserts that the fact that an enzyme can catalyze the conversion of AL to DHIV “using NADPH” does not, on its own, indicate that the enzyme cannot also use other cofactors, such as NADH, to catalyze that conversion. Gevo argues that Butamax’s interpretation reads out an important aspect of the patentees’ definition of KARI because all KARI are capable of using NADPH as a cofactor. Thus, Gevo argues it would have been completely unnecessary for the patents to have referred to “using NADPH” in the first instance. Gevo also argues that the phrase “using NADPH” must be understood in light of other aspects of the specifications. Gevo first contends that the specifications use the term “use(s) NADPH” interchangeably with the phrase “NADPH-dependent.” Gevo points to this passage: 14 BUTAMAX(TM) ADVANCED BIOFUELS v. GEVO, INC. [A]lcohol dehydrogenase VI (ADH6) and Ypr1p . . . use NADPH as electron donor. An NADPH- dependent reductase, YqhD, . . . has also been re- cently identified in E. coli . . . . ’188 Patent col. 12 ll. 50–60. The patents further describe ADH6 as “NADPH-dependent cinnamyl alcohol dehydrogenase.” Id. at col. 4 ll. 60–62. However, “[i]t is not enough for a patentee to simply disclose a single embodiment or use a word in the same manner in all embodi- ments.” Thorner, 669 F.3d at 1365. We agree with Butamax and find no reason to con- strict the phrase “using NADPH” to mean “only use NADPH” or “NADPH-dependent.” We also disagree with Gevo’s argument that such an interpretation reads out an important part of the patentees’ definition. The patents’ definition at least excludes as-yet-undiscovered KARI enzymes that could catalyze the conversion of AL to DHIV without using NADPH at all. Moreover, the description of specific types of KARI as NADPH-dependent does not clearly express an intent to redefine all KARI “using NADPH” as KARI that must be NADPH-dependent. Next, Gevo points to the patents’ descriptions of other enzymes that use or utilize either NAD+ or “NADH . . . and/or NADPH” as an electron donor. Id. at col. 8 ll. 14– 16, 25–29. Gevo contends that the patentees knew how to describe enzymes that used NADH or both NADH and NADPH and that the patentees instead chose to define KARI as using only NADPH. Butamax counters that the patents’ descriptions of other enzymes “using” or “utilizing” various cofactors merely is a reference to particular EC numbers or the assays for the enzymes in question. For example, Butamax contends that the standard assay for KARI is the Arfin-Umbarger assay, which “uses” NADPH to measure KARI activity by monitoring the consumption of NADPH in the presence of acetolactate and the enzyme in quesBUTAMAX(TM) ADVANCED BIOFUELS v. GEVO, INC. 15 tion. Appellant’s Br. 14. The patents’ Example 2 expressly teaches to measure KARI activity “using the method described by Arfin and Umbarger,” ’188 Patent col. 33 ll. 45–47. Example 10 teaches using the same method. Id. at col. 39 ll. 4–5. Butamax also argues that the patents’ reference to “using NADPH” merely matches the description of the enzyme in EC number 1.1.1.86, which notes the use of NADP+ but is silent as to NAD+ or NADH. Butamax notes that the other enzymes in question from the specifications have multiple EC numbers—each referring to NADH, NADPH, or both NADH and NADPH—and/or have multiple different assays for their identification—each assay using a different cofactor. Thus, Butamax argues that the patentees merely referred the other cofactors where appropriate. Appellant’s Br. 45. We agree with Butamax that the references to other enzymes as either using NAD+ or using NADH and/or NADPH do not imply that the patentees intended to limit KARI’s use of NADH. The patentees’ description of KARI merely corresponds with the Arfin-Umbarger assay and the description of KARI in EC Number 1.1.1.86.