Ex Parte Rahman et al

Patent Trial and Appeal BoardMar 22, 2016

12424897 (P.T.A.B. Mar. 22, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE APPLICATION NO. FILING DATE 12/424,897 04/16/2009 62008 7590 03/24/2016 MAIER & MAIER, PLLC 345 South Patrick Street ALEXANDRIA, VA 22314 FIRST NAMED INVENTOR Raja N. Rahman UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www .uspto.gov ATTORNEY DOCKET NO. CONFIRMATION NO. 01940011US 1453 EXAMINER STEADMAN, DAVID J ART UNIT PAPER NUMBER 1656 NOTIFICATION DATE DELIVERY MODE 03/24/2016 ELECTRONIC Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address( es): patent@maierandmaier.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte RAJAN. RAHMAN, ABU B. SALLER, MAHIRAN BASRI, and THEAN C. LEOW Appeal2014-000433 Application 12/424,8971 Technology Center 1600 Before LORA M. GREEN, JEFFREY N. FREDMAN, and RYAN H. FLAX, Administrative Patent Judges. FLAX, Administrative Patent Judge. DECISION ON APPEAL This is a decision on appeal under 35 U.S.C. Â§ 134(a) involving claims directed to a purified Geobacillus sp. strain T 1 lipase enzyme crystal (and a composition comprising such a crystal). The Examiner rejects claims 1 and 4 as indefinite, as drawn to subject matter not supported by the written description, and as obvious. We have jurisdiction under 35 U.S.C. Â§ 6(b). We AFFIRM. 1 According to Appellants, the real party in interest are the above-named inventors. (App. Br. at 2). Appeal2014-000433 Application 12/424,897 STATEMENT OF THE CASE Claims 1 and 4 of U.S. Patent Application No. 12/424,8972 are on appeal. These claims can be found in the Claims Appendix of the Appeal Brief. Independent claim 1 is representative of the claims on appeal and reads as follows: 1. A purified Geobacillus sp. strain Tl lipase enzyme crystal obtained from a method comprising a) providing purified, mature Geobacillus sp. strain Tl lipase from Geobacillus sp. strain Tl to be crystallized, b) preparing a crystallization mix comprising a buffer comprising 0.1 M NaH2P04, 0.1 M KH2P04, and 0.1 M MES pH 6.5, wherein said buffer comprises between 0.5 to 4.5 mg/mL of lipase from step (a), and wherein said buff er comprises between 1 and 2M of precipitant, wherein said precipitant is NaCl, and c) obtaining Geobacillus sp. strain T 1 lipase crystals from step (b) by a hanging-drop methodology, wherein crystals of the lipase are formed between about 1 hour and 1 day. (App. Br. 21, Claims Appendix). The claims on appeal stand rejected as follows: A. Claims 1 and 4 under 35 U.S.C. Â§ 112, second paragraph, as being indefinite in the recitation of "mature Geobacillus sp. strain Tl lipase from Geobacillus sp. strain Tl"; 2 Hereinafter "the appealed application." All references to the disclosure of the appealed application are to the "Specification" or "Spec" of application Publication No. US 2009/0197318 Al, published Aug. 6, 2009. 2 Appeal2014-000433 Application 12/424,897 B. Claims 1 and 4 under 35 U.S.C. Â§ 112, first paragraph, for failing to meet the written description requirement "because the specification fails to describe the claimed method of crystallizing a 'mature Tl lipase from Geobacillus sp. strain Tl"'; and C. Claims 1 and 4 under 35 U.S.C. Â§ 103(a) as being unpatentable over Salleh3, McPherson4, Li5, and Jeong. 6 FINDINGS OF FACT FF 1. Salleh discloses "the deduced mature [Geo bacillus sp. strain Tl] lipase [is] composed of 388 amino acids which correspond to a molecular Mass of 43.195 kDa" and "[the deduced mature Geobacillus sp. strain T 1] polypeptide was composed of a signal peptide (2 8 amino acids) and a mature protein of 388 amino acids." (Salleh 497, 495, respectively; see also, Ans. 6 (Examiner noted same disclosure of Salleh). 3 Salleh et al., Structural Elucidation of Thermostable Lipase from a new Species ofGeobacillus sp. Tl, in 17 BIOTECHNOLOGY FOR SUSTAINABLE UTILIZATION OF BIOLOGICAL RESOURCES IN THE TROPICS 495--498 (2004) (hereinafter "Salleh"). 4 Alexander McPherson, Current Approaches to Macromolecular Crystallization, 189 EUR. J. BIOCHEM. 1-23 (1990) (hereinafter "McPherson"). 5 Li et al., Crystal Structure of the Escherichia coli Thioesterase IL a Homo log of the Human Nef Binding Enzyme, 7 NATURE STRUCTURAL BIO. 555-559 (2000) (hereinafter "Li"). 6 Jeong et al., Crystallization and Preliminary X-ray Analysis of Thermoalkalophilic Lipase from Bacillus Stearothermophilus LI, D57 ACTA CRYSTALLOGRAPHICA 1300-1302 (2001) (hereinafter "Jeong"). 3 Appeal2014-000433 Application 12/424,897 FF2. Salleh discloses "expression of T 1 lipase including signal peptide was achieved through prokaryotic system involving ... pGEX-4T ..... " (Id. at 496). FF3. Leow discloses "the deduced mature [Geo bacillus sp. strain T 1] lipase was composed of 3 8 8 amino acids, which corresponds to a molecular mass of 43.195 kDa." (Leow 99; see also, Ans. 6 (Examiner noting Leow's disclosure of a 388 amino acid lipase, like Salleh). 7 FF4. Leow discloses expression of Geobacillus sp. strain Tl using thermostable Tl lipase gene "subcloned into pGEX-4Tl vector for fusion protein expression" including thrombin cleavage. (Leow 101, Fig. 4; see also, Final Action 5 (discussing Leow)). FF5. Matsumura discloses "obtain[ing] pure mature [ Geobacillus zalihae strain] T 1 lipase" using "recombinant plasmid pGEX/TlS." (Matsumura 593; see also, Supp. App. Br. 6 (discussing Matsumura)).8 FF6. Matsumura discloses "models of wild-type ... enzymes ... include 776 amino acid residues (for two molecules)," that is, 338 amino 7 Leow et al., High Level Expression of Thermostable Lipase from Geobacillus sp. Strain Tl, BIOSCI. BIOTECHNOL. BIOCHEM. 96-103 (2004) (hereinafter "Leow"). 8 Matsumura, et al., Novel Cation-Jr Interaction Revealed by Crystal Structure of Thermoalkalophilic Lipase, WILEY lNTERSCIENCE (Oct. 11, 2007) (hereinafter "Matsumura"). Note, this reference is also referred to within the appealed application's file history and appeal briefing as "Leow et al., Proteins: Structure, Function, and bioinformatics, 70: 592-598 (2008)." (See, e.g., Supp. App. Br. 16). 4 Appeal2014-000433 Application 12/424,897 acid residues for one molecule of Geobacillus zalihae strain Tl lipase. (Matsumura 595; see also, Supp. App. Br. 6-7 (discussing Matsumura)). FF7. Salleh discloses a purified, mature Geobacillus sp. T 1 lipase enzyme crystal and a process for producing the same. (Salleh 496-8, Fig. 4; see also, Ans. 18-19 (noting the Salleh crystal unit cell data). FF8. The crystal structure of a purified, mature Geobacillus sp. strain T 1 lipase enzyme crystal obtained by the process disclosed by Salleh can be defined by the following data: a= 117.31 A b =81.04A c = 99.22 A fJ = 96.91Â° Volume: 943,246,943 (A3) (See Salleh 498; see also, Appellants' Office Action Resp. filed June 23, 2011 6-7 and the accompanying Second Declaration Under 37 C.F.R. Â§ 1.132 by Raja N. Rahman dated June 17, 2011 at 2 (hereinafter "the Rahman Deel.") (each identifying this crystal). FF9. Matsumura discloses a process for crystallizing a "pure mature Tl lipase [from Geobacillus zalihae strain Tl]" under the following conditions: "drops containing 3 ÂµL protein at 2 mg mL-1 in 50 mMTris-HCl pH 8.0 and 3 ÂµL precipitating buffer were equilibrated against 500 ÂµL of precipitating buffer containing 0.5MNaCl, O. lMKH2P04, O. lMNaH2P04, and O. lMMES buffer pH 6.6" and that "[t]he crystals typically grew to a maximum size of0.3 X 0.3 X O.l mm3 over 1 week." (Matsumura 593--4; see also, Supp. App. Br. 6-7 (citing same portion of Matsumura)). 5 Appeal2014-000433 Application 12/424,897 FFlO. The crystal structure of a purified, mature Geobacillus sp. strain T 1 lipase enzyme crystal obtained by the process disclosed by Matsumura can be defined by the following data: a= 117.73 A b = 81.27A c = 99.91 A fJ = 97.09Â° (Matsumura 594). FFl 1. McPherson discloses that "[t]here are even cases where the identical protein prepared by different procedures or at different times may show significant variations [in crystal formation]." (McPherson 13; see also, Ans. 20 (discussing McPherson)). FF12. Claim 1 recites a range of "mature Geo bacillus sp. strain Tl lipase from Geobacillus sp. strain Tl to be crystallized," that is, "between 0.5 to 4.5 mg/mL of lipase." FF13. Claim 1 recites a range of crystallization mix precipitant concentrations, that is, "between 1 and 2M of precipitant, wherein said precipitant is NaCL" FF14. The appealed claims do not recite a specific crystal structure or specific unit cell dimensions. 6 Appeal2014-000433 Application 12/424,897 DISCUSSION A. and B. The rejections of claims 1 and 4 under 35 U.S.C. Â§ 112, second paragraph, as being indefinite in the recitation of "mature Geobacillus sp. strain Tl lipase from Geobacillus sp. strain Tl" and under 35 U.S.C. Â§ 112, first paragraph, for failing to meet the written description requirement "because the specification fails to describe the claimed method of crystallizing a 'mature Tl lipase from Geobacillus sp. strain Tl"' The Examiner's rejections under 35 U.S.C. Â§ 112, paragraphs 1 and 2, hinge upon the same facts and so we consider these issues together. (See Ans. 5-11 ). The question presented is whether the claim term "mature Geobacillus sp. strain T 1 lipase from Geobacillus sp. strain Tl" would have been understood by the person of ordinary skill in the art to refer to the 388 amino acid polypeptide disclosed in Salleh. (See Salleh 496-7, Fig. 2). We find that a person of ordinary skill in the art would understand the claim term as referring to the protein as disclosed by Salleh. The Examiner determined that the term "mature Geobacillus sp. strain Tl lipase from Geobacillus sp. strain Tl" is indefinite because it is unclear as to the scope of polypeptides encompassed by the term. (See Final Action 2; Ans. 5). The Examiner determined that the claim term was used in the already-of-record Salleh reference. (Final Action 2; Ans. 5). The Examiner determined (see Ans. 6) that Salleh identified "mature Geobacillus sp. strain Tl lipase" as follows: [t]he putative signal peptide cleavage site was located at between Ala-28 and Ala-29 .... Therefore, the deduced mature lipase composed of 3 88 amino acids which correspond to a molecular Mass of 43.195 kDa. [and] 7 Appeal2014-000433 Application 12/424,897 The polypeptide was composed of a signal peptide (28 amino acids) and a mature protein of 388 amino acids. (Salleh 497 and 495, respectively). Finally, the Examiner determined (Ans. 6) that one of ordinary skill in the art would have understood the claim term at issue to mean a 388 amino acid polypeptide having the sequence of amino acids 29--416 as shown at Fig. 2 of Salleh, which is reproduced below: MKCCRJMFVLLGLWFVâ€¢"GLSVPGGRTEAASLRANDAPlVLLHGfl"TG\.V GREJ:MFGFKY\VGGVRGDIEQ\VLNDNGYRTb'TLAVGPLSSN\VDRACEA VAQLVGGTVDVGAAHAAKHGHARFGRTYPGLLPELKRGGRlHIIAHSQ GGQTARMLVSLLENGSQEEREYAKAHNVSLSPLFEGGHHFVLSVTIIAT PHDGTTLVNMVDFTDRFFDLQKAVLto:AAAYASNVPYTSQVYIU.KLDQ\Y GLRRQPGESFDIJYFERLKRSPVWTSTDTARYDLSVSGAEKLNQWVQAS PNTYYLSFSTERTYRGALTGNHYPELGMNAFSAVVCAPFLGSYRNPTLG IDDRWLENDGfVNTVSMNGPKRGSSDRIVPVDGTLKKGVWNDMGTYN VDHLEJlGVDPNPSFDIRAFYLRLAEQLASLQP Molecular weight:4Q.4 kDa Amino acids: 416rt:siducs Nucl~otides'. 1,25 I hp Signaf J)fptide: 1MetÂ·28Ala Fig, 2. Tlte umfno ::idd sequente$ Md analysis of tlte Tl lipase gene from <.it.'