Patents by Inventor Xiyun Zhang

Xiyun Zhang has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Cellobiohydrolase variants
    Patent number: 9260705
    Abstract: The present invention relates to cellobiohydrolase variants having improved thermostability in comparison to wild-type CBH2a.
    Type: Grant
    Filed: December 31, 2014
    Date of Patent: February 16, 2016
    Assignee: Codexis, Inc.
    Inventors: Dipnath Baidyaroy, Louis Clark, David Elgart, Rama Voladri, Xiyun Zhang
  • PENTOSE FERMENTATION BY A RECOMBINANT MICROORGANISM
    Publication number: 20160040139
    Abstract: The present invention provides methods and compositions suitable for use in the conversion of xylose to xylitol and xylulose, including nucleic acid constructs, recombinant fungal host cells, and related materials.
    Type: Application
    Filed: October 26, 2015
    Publication date: February 11, 2016
    Inventors: Xiyun Zhang, Ryan C. Fong, Ezhilkani Subbian
  • NOVEL P450-BM3 VARIANTS WITH IMPROVED ACTIVITY
    Publication number: 20160010065
    Abstract: The present invention provides improved P450-BM3 variants with improved activity. In some embodiments, the P450-BM3 variants exhibit improved activity over a wide range of substrates.
    Type: Application
    Filed: July 8, 2015
    Publication date: January 14, 2016
    Inventors: Robert Osborne, Vesna Mitchell, Khin Yu Naing Htwe, Xiyun Zhang, Erika M. Milczek, Jeffrey C. Moore
  • PENTOSE FERMENTATION BY A RECOMBINANT MICROORGANISM
    Publication number: 20160010132
    Abstract: The present invention provides recombinant nucleic acid constructs comprising a xylose isomerase polynucleotide, a recombinant fungal host cell comprising a recombinant xylose isomerase polynucleotide, and related methods.
    Type: Application
    Filed: September 30, 2015
    Publication date: January 14, 2016
    Inventors: Ezhilkani Subbian, Xiyun Zhang, Benjamin N. Mijts, Catherine M. Cho
  • Synthesis of prazole compounds
    Patent number: 9228216
    Abstract: The present disclosure relates to non-naturally occurring monooxygenase polypeptides useful for preparing prazole compounds, polynucleotides encoding the polypeptides, and methods of using the polypeptides.
    Type: Grant
    Filed: October 30, 2014
    Date of Patent: January 5, 2016
    Assignee: Codexis, Inc.
    Inventors: Yong Koy Bong, Michael D. Clay, Steven J. Collier, Benjamin Mijts, Michael Vogel, Xiyun Zhang, Jun Zhu, Jovana Nazor, Derek J. Smith, Shiwei Song
  • RECOMBINANT FUNGAL POLYPEPTIDES
    Publication number: 20150337279
    Abstract: The invention relates to Myceliophthora thermophila biomass degradation polypeptides and Myceliophthora thermophila polypeptides that increase protein productivity, nucleic acids encoding such polypeptides, and methods of producing the polypeptides. The invention further relates to methods for degrading a cellulosic biomass using a biomass degradation polypeptide and methods of engineering a cell or methods of increasing protein production using a polypeptide of the invention.
    Type: Application
    Filed: November 19, 2013
    Publication date: November 26, 2015
    Inventors: Xiyun Zhang, Dipnath Baidyaroy
  • ENONE REDUCTASES
    Publication number: 20150315613
    Abstract: The disclosure relates to engineered enone reductase polypeptides having improved properties, polynucleotides encoding the engineered polypeptides, related vectors, host cells, and methods for making the engineered enone reductase polypeptides. The disclosure also provides methods of using the engineered enone reductase polypeptides for chemical transformations.
    Type: Application
    Filed: July 15, 2015
    Publication date: November 5, 2015
    Inventors: Christopher K. Savile, Vesna Mitchell, Xiyun Zhang, Gjalt W. Huisman
  • Pentose fermentation by a recombinant microorganism
    Patent number: 9169468
    Abstract: The present invention provides methods and compositions suitable for use in the conversion of xylose to xylitol and xylulose, including nucleic acid constructs, recombinant fungal host cells, and related materials.
    Type: Grant
    Filed: January 14, 2014
    Date of Patent: October 27, 2015
    Assignee: Codexis, Inc.
    Inventors: Xiyun Zhang, Ryan C. Fong, Ezhilkani Subbian
  • ENGINEERED TYROSINE AMMONIA LYASE
    Publication number: 20150299689
    Abstract: The present invention provides engineered tyrosine ammonia-lyase (TAL) polypeptides and compositions thereof. In some embodiments, the engineered TAL polypeptides have been optimized to provide enhanced catalytic activity while reducing sensitivity to proteolysis and increasing tolerance to acidic pH levels. The invention also provides methods for utilization of the compositions comprising the engineered TAL polypeptides for therapeutic and industrial purposes.
    Type: Application
    Filed: April 16, 2015
    Publication date: October 22, 2015
    Inventors: Gjalt W. Huisman, Nicholas J. Agard, David Elgart, Xiyun Zhang
  • Beta-glucosidase variants
    Patent number: 9150843
    Abstract: The invention relates to recombinantly produced ?-glucosidase variants with enhanced thermoactivity compared to naturally occurring proteins. The invention also provides methods for producing a variant ?-glucosidase polypeptide with improved thermoactivity by identifying performance sensitive positions in a target ?-glucosidase polypeptide and substituting the residue at that position with a thermoactivity enhancing residue.
    Type: Grant
    Filed: November 13, 2014
    Date of Patent: October 6, 2015
    Assignee: Codexis, Inc.
    Inventors: Xiyun Zhang, Jie Yang, Dipnath Baidyaroy, Sally R. Postlethwaite, Attila Andor, Louis A. Clark, Lisa Marie Newman
  • Enone reductases
    Patent number: 9121045
    Abstract: The disclosure relates to engineered enone reductase polypeptides having improved properties, polynucleotides encoding the engineered polypeptides, related vectors, host cells, and methods for making the engineered enone reductase polypeptides. The disclosure also provides methods of using the engineered enone reductase polypeptides for chemical transformations.
    Type: Grant
    Filed: October 2, 2014
    Date of Patent: September 1, 2015
    Assignee: Codexis, Inc.
    Inventors: Christopher K. Savile, Vesna Mitchell, Xiyun Zhang, Gjalt W. Huisman
  • VARIANT ENDOGLUCANASES AND RELATED POLYNUCLEOTIDES
    Publication number: 20150218541
    Abstract: The invention provides variants of the Clostridium thermocellum endoglucanase (CelG) that have improved endoglucanase activity compared to the wild type enzyme. Also provided are related polynucleotides, compositions, vectors, host cells, and methods of use.
    Type: Application
    Filed: March 9, 2015
    Publication date: August 6, 2015
    Inventors: Jie Yang, Xiyun Zhang, Ish K. Dhawan, Andrew Shaw
  • TRANSAMINASE POLYPEPTIDES
    Publication number: 20150210988
    Abstract: The present disclosure provides engineered transaminase enzymes having improved properties as compared to a naturally occurring wild-type transaminase enzyme. Also provided are polynucleotides encoding the engineered transaminase enzymes, host cells capable of expressing the engineered transaminase enzymes, and methods of using the engineered transaminase enzymes to synthesize a variety of chiral compounds.
    Type: Application
    Filed: April 13, 2015
    Publication date: July 30, 2015
    Inventors: Ish K. Dhawan, Gregory Miller, Xiyun Zhang
  • CELLOBIOHYDROLASE VARIANTS
    Publication number: 20150197736
    Abstract: The present invention relates to cellobiohydrolase variants having improved thermostability in comparison to wild-type CBH2a.
    Type: Application
    Filed: December 31, 2014
    Publication date: July 16, 2015
    Inventors: DIPNATH BAIDYAROY, LOUIS CLARK, DAVID ELGART, RAMA VOLADRI, XIYUN ZHANG
  • FUNGAL BETA-XYLOSIDASE VARIANTS
    Publication number: 20150191759
    Abstract: The present invention provides fungal xylanase and/or beta-xylosidase enzymes suitable for use in saccharification reactions. The present application further provides genetically modified fungal organisms that produce xylanase and/or beta-xylosidases, as well as enzyme mixtures exhibiting enhanced hydrolysis of cellulosic material to fermentable sugars, enzyme mixtures produced by the genetically modified fungal organisms, and methods for producing fermentable sugars from cellulose using such enzyme mixtures.
    Type: Application
    Filed: March 3, 2015
    Publication date: July 9, 2015
    Inventors: Ryan Fong, Xiyun Zhang, Chris Noriega, Nicholas Agard, Anupam Gohel, Derek Smith
  • ENDOGLUCANASE VARIANTS
    Publication number: 20150140641
    Abstract: The present invention relates to variant endoglucanases having improved thermoactivity, improved thermostability, and improved viscosity reduction activity over wild-type M. thermophila endoglucanase.
    Type: Application
    Filed: November 14, 2014
    Publication date: May 21, 2015
    Inventors: XIYUN ZHANG, SACHIN PATIL, JIE YANG, ISH KUMAR DHAWAN
  • AUTOMATED SCREENING OF ENZYME VARIANTS
    Publication number: 20150133307
    Abstract: Disclosed are methods for identifying bio-molecules with desired properties (or which are most suitable for a round of directed evolution) from complex bio-molecule libraries or sets of such libraries. Some embodiments of the present disclosure provide methods for virtually screening proteins for beneficial properties. Some embodiments of the present disclosure provide methods for virtually screening enzymes for desired activity and/or selectivity for catalytic reactions involving particular substrates. Some embodiments combine screening and directed evolution to design and develop proteins and enzymes having desired properties. Systems and computer program products implementing the methods are also provided.
    Type: Application
    Filed: September 26, 2014
    Publication date: May 14, 2015
    Inventors: Xiyun Zhang, Russell Javiniar Sarmiento, Donald Scott Baskerville, Gjalt W. Huisman
  • STRUCTURE BASED PREDICTIVE MODELING
    Publication number: 20150134315
    Abstract: Disclosed are methods for building a sequence activity model with reference to structural data, which model can be used to guide directed evolution of proteins having beneficial properties. Some embodiments use genetic algorithms and structural data to filter out uninformative data. Some embodiments use a support vector machine to train the sequence activity model. The filtering and training methods can generate a sequence activity model having higher predictive power than conventional modeling methods. Systems and computer program products implementing the methods are also provided.
    Type: Application
    Filed: September 26, 2014
    Publication date: May 14, 2015
    Inventors: Russell Javiniar Sarmiento, Donald Scott Baskerville, Xiyun Zhang
  • Transaminase polypeptides
    Patent number: 9029106
    Abstract: The present disclosure provides engineered transaminase enzymes having improved properties as compared to a naturally occurring wild-type transaminase enzyme. Also provided are polynucleotides encoding the engineered transaminase enzymes, host cells capable of expressing the engineered transaminase enzymes, and methods of using the engineered transaminase enzymes to synthesize a variety of chiral compounds.
    Type: Grant
    Filed: June 18, 2013
    Date of Patent: May 12, 2015
    Assignee: Codexis, Inc.
    Inventors: Ish K. Dhawan, Gregory Miller, Xiyun Zhang
  • Variant endoglucanases and related polynucleotides
    Patent number: 9005946
    Abstract: The invention provides variants of the Clostridium thermocellum endoglucanase (CelG) that have improved endoglucanase activity compared to the wild type enzyme. Also provided are related polynucleotides, compositions, vectors, host cells, and methods of use.
    Type: Grant
    Filed: March 10, 2010
    Date of Patent: April 14, 2015
    Assignee: Codexis, Inc.
    Inventors: Jie Yang, Xiyun Zhang, Ish Kumar Dhawan, Andrew Shaw