Ostermeier, Marc

Professor
Chemical And Biomolecular Engineering

Maryland Hall 119
(410) 516-7144
oster@jhu.edu

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Ostermeier Elected to AIMBE College of Fellows

January 22, 2014

Marc Ostermeier, professor of chemical and biomolecular engineering, has been elected to the American Institute for Medical and Biological Engineering’s 2014 College of Fellows. AIMBE’s College of Fellows comprises a select group of about 1,500 people who have made significant and transformational contributions to medical and biological engineering. Ostermeier was recognized for his work on […]

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About

Education
  • Ph.D. 1996, Univ Texas Austin*
Experience
  • 2014 - 2017:  Member, Homewood Academic Council, The Johns Hopkins University
  • 2011 - 2013:  Vice Chair, WSE Chemical and Biomolecular Engineering
  • 2008 - 2011:  Director of the Graduate Program, WSE Chemical and Biomolecular Engineering
  • 2005 - 2008:  Director of the Undergraduate Program, WSE Chemical and Biomolecular Engineering
  • 1996 - 2000:  Postdoctoral Fellow, Pennsylvania State Univ University Park
Awards
  • 2014:  Fellow, AIMBE
  • 2005:  Keynote Address - Protein Engineering: Defining the Next Generation of Biotherapeutics (IBC International Conference) San Diego - CA.
  • 2003:  NSF CAREER Award
  • 1999:  Conference Fellowship - United Engineering Foundation - Enzyme Engineering XV
  • 1997:  NIH Postdoctoral Fellowship
  • 1991:  University of Texas at Austin Competitive Graduate Scholarship
  • 1990:  Tau Beta Pi Engineering Honorary Society
  • 1985:  New Mexico Institute of Mining and Technology Institutional Scholarship

Publications

Journal Articles
  • Warren TD, Patel K, Rivera JL, Ostermeier M (2018).  Comprehensive mutagenesis on yeast cytosine deaminase yields improvements in 5-fluorocytosine toxicity in HT1080 cells.  AIChE Journal.  (Invited article for special issue honoring Frances Arnold's Nobel Prize in Chemistry).
  • Gonzalez CE, Roberts P, Ostermeier M (2018).  Fitness effects of single amino acid insertions and deletions in TEM-1 β-lactamase.  Journal of Molecular Biology.
  • Gonzalez CE, Ostermeier M (2018).  Pervasive pairwise intragenic epistasis among sequential mutations in TEM-1 β-lactamase.  Journal of Molecular Biology.
  • Warren TD, Patel K, Ostermeier M (2018).  Protein-programmed accumulation of yeast cytosine deaminase in cancer cells in response to mock-hypoxia.  Protein Engineering Design and Selection.
  • Ribeiro L, Chelius C, Boppidi K, Naik N, Hossain S, Ramsey J, Kumar J, Riberio L, Ostermeier M, Tran B, Goo Y, deAssis L, Ulas M, Bayram Ö, Goldman G, Lincoln S, Srivastava R, Harris S, Marten M (2018).  Comprehensive analysis of A. nidulans PKA phosphorylome identifies a novel mode of CreA regulation.  mBio.
  • Xiong T, Rohm D, Workman RE, Roundtree L, Novina CD, Timp W, Ostermeier M (2018).  Protein engineering strategies for improving the selective methylation of target CpG sites by a dCas9-directed cytosine methyltransferase in bacteria.  PLoS ONE.  13(12).
  • Ko CC, Ostermeier M, Lin SC (2018).  Dual column approach for the purification of zinc finger proteins by immobilized metal affinity chromatography.  Process Biochemistry.  73.  204-210.
  • Xiong T, Meister GE, Workman RE, Kato NC, Spellberg MJ, Turker F, Timp W, Ostermeier M, Novina CD (2017).  Targeted DNA methylation in human cells using engineered dCas9-methyltransferases.  Scientific Reports.  7(1).
  • Shelat NY, Parhi S, Ostermeier M (2017).  Development of a cancer-marker activated enzymatic switch from the herpes simplex virus thymidine kinase.  Protein Engineering, Design and Selection.  30(2).  95-103.
  • Ribeiro LF, Warren TD, Ostermeier M (2017).  Construction of protein switches by domain insertion and directed evolution..  Methods in molecular biology.  1596.  43-55.
  • Hauk P, Stephens K, McKay R, Virgile CR, Ueda H, Ostermeier M, Ryu KS, Sintim HO, Bentley WE (2016).  Insightful directed evolution of Escherichia coli quorum sensing promoter region of the lsrACDBFG operon: A tool for synthetic biology systems and protein expression.  Nucleic Acids Research.  44(21).  10515-10525.
  • Shelat NY, Parhi S, Ostermeier M (2016).  A positive selection for nucleoside kinases in E. coli.  PLoS ONE.  11(9).
  • Choi JH, Xiong T, Ostermeier M (2016).  The interplay between effector binding and allostery in an engineered protein switch.  Protein Science.  1605-1616.
  • Steinberg B, Ostermeier M (2016).  Shifting Fitness and Epistatic Landscapes Reflect Trade-offs along an Evolutionary Pathway.  Journal of Molecular Biology.  428(13).  2730-2743.
  • Tullman J, Nicholes N, Dumont MR, Ribeiro LF, Ostermeier M (2016).  Enzymatic protein switches built from paralogous input domains.  Biotechnology and Bioengineering.  113(4).  852-858.
  • Fuenzalida JP, Nareddy PK, Moreno-Villoslada I, Moerschbacher BM, Swamy MJ, Pan S, Ostermeier M, Goycoolea FM (2016).  On the role of alginate structure in complexing with lysozyme and application for enzyme delivery.  Food Hydrocolloids.  53.  239-248.
  • Choi JH, Zayats M, Searson PC, Ostermeier M (2016).  Electrochemical activation of engineered protein switches.  Biotechnology and Bioengineering.  113(2).  453-456.
  • Meister G, Xiong T, Ostermeier M, Novina C (2016).  Site-specific DNA methylation in human cells using engineered CAS9-methyltransferases.  Synthetic Biology: Engineering, Evolution, and Design Conference 2016, SEED 2016.  141-153.
  • Ribeiro LF, Tullman J, Nicholes N, Silva SRB, Vieira DS, Ostermeier M, Ward RJ (2016).  A xylose-stimulated xylanase-xylose binding protein chimera created by random nonhomologous recombination.  Biotechnology for Biofuels.  9(1).
  • Steinberg B, Ostermeier M (2016).  Environmental changes bridge evolutionary valleys.  Science Advances.  2(1).
  • Ribeiro LF, Nicholes N, Tullman J, Ribeiro LFC, Fuzo CA, Vieira DS, Furtado GP, Ostermeier M, Ward RJ (2015).  Insertion of a xylanase in xylose binding protein results in a xylose-stimulated xylanase.  Biotechnology for Biofuels.  8(1).
  • Nicholes N, Date A, Beaujean P, Hauk P, Kanwar M, Ostermeier M (2015).  Modular protein switches derived from antibody mimetic proteins.  Protein Engineering, Design and Selection.  29(2).  77-85.
  • Choi JH, Laurent AH, Hilser VJ, Ostermeier M (2015).  Design of protein switches based on an ensemble model of allostery.  Nature Communications.  6.
  • Cheung LSL, Shea DJ, Nicholes N, Date A, Ostermeier M, Konstantopoulos K (2015).  Characterization of Monobody Scaffold Interactions with Ligand via Force Spectroscopy and Steered Molecular Dynamics.  Scientific Reports.  5.
  • Choi JH, Ostermeier M (2015).  Rational design of a fusion protein to exhibit disulfide-mediated logic gate behavior.  ACS Synthetic Biology.  4(4).  400-406.
  • Russell JH, Ostermeier M (2014).  The thymidylate kinase genes from Mycobacterium tuberculosis and methicillin-resistant Staphylococcus aureus confer 3'-azido-3'-deoxythymidine resistance to Escherichia coli..  FEMS Microbiology Letters.  361(2).  158-65.
  • Wright RC, Khakhar A, Eshleman JR, Ostermeier M (2014).  Advancements in the development of hif-1a-activated protein switches for use in enzyme prodrug therapy e114032.  PLoS ONE.  9(11).
  • Chaikind B, Ostermeier M (2014).  Directed evolution of improved zinc finger methyltransferases.  PLoS ONE.  9(5).
  • Firnberg E, Labonte JW, Gray JJ, Ostermeier M (2014).  A comprehensive, high-resolution map of a Gene's fitness landscape.  Molecular Biology and Evolution.  31(6).  1581-1592.
  • Valdes G, Schulte RW, Ostermeier M, Iwamoto KS (2014).  The high-affinity maltose switch MBP317-347 has low affinity for glucose: Implications for targeting tumors with metabolically directed enzyme prodrug therapy.  Chemical Biology and Drug Design.  83(3).  266-271.
  • Firnberg E, Ostermeier M (2013).  The genetic code constrains yet facilitates Darwinian evolution.  Nucleic Acids Research.  41(15).  7420-7428.
  • Choi JH, San A, Ostermeier M (2013).  Non-allosteric enzyme switches possess larger effector-induced changes in thermodynamic stability than their non-switch analogs.  Protein Science.  22(4).  475-485.
  • Kanwar M, Wright RC, Date A, Tullman J, Ostermeier M (2013).  Protein switch engineering by domain insertion.  Methods Enzymol.  523.  369-88.
  • Firnberg E, Ostermeier M (2012).  PFunkel: Efficient, Expansive, User-Defined Mutagenesis.  PLoS ONE.  7(12).
  • Chaikind B, Kilambi KP, Gray JJ, Ostermeier M (2012).  Targeted DNA Methylation Using an Artificially Bisected M.HhaI Fused to Zinc Fingers.  PLoS ONE.  7(9).
  • Ke W, Laurent AH, Armstrong MD, Chen Y, Smith WE, Liang J, Wright CM, Ostermeier M, van den Akker F (2012).  Structure of an engineered β-lactamase maltose binding protein fusion protein: Insights into heterotropic allosteric regulation.  PLoS ONE.  7(6).
  • Guntas G, Kanwar M, Ostermeier M (2012).  Circular permutation in the ω-loop of TEM-1 β-lactamase results in improved activity and altered substrate specificity.  PLoS ONE.  7(4).
  • Cheung LSL, Kanwar M, Ostermeier M, Konstantopoulos K (2012).  A hot-spot motif characterizes the interface between a designed ankyrin-repeat protein and its target ligand.  Biophysical Journal.  102(3).  407-416.
  • Heins RA, Choi JH, Sohka T, Ostermeier M (2011).  In vitro recombination of non-homologous genes can result in gene fusions that confer a switching phenotype to cells.  PLoS ONE.  6(11).
  • Tullman J, Guntas G, Dumont M, Ostermeier M (2011).  Protein switches identified from diverse insertion libraries created using S1 nuclease digestion of supercoiled-form plasmid DNA.  Biotechnology and Bioengineering.  108(11).  2535-2543.
  • Wright CM, Wright RC, Eshleman JR, Ostermeier M (2011).  A protein therapeutic modality founded on molecular regulation.  Proceedings of the National Academy of Sciences of the United States of America.  108(39).  16206-16211.
  • Zayats M, Kanwar M, Ostermeier M, Searson PC (2011).  Molecular imprinting of maltose binding protein: Tuning protein recognition at the molecular level.  Macromolecules.  44(10).  3966-3972.
  • Zayats M, Kanwar M, Ostermeier M, Searson PC (2011).  Surface-tethered protein switches.  Chemical Communications.  47(12).  3398-3400.
  • Ostermeier M, Berlin MA, Meudtner RM, Demeshko S, Meyer F, Limberg C, Hecht S (2010).  Complexes of click-derived bistriazolylpyridines: Remarkable electronic influence of remote substituents on thermodynamic stability as well as electronic and magnetic properties.  Chemistry - A European Journal.  16(33).  10202-10213.
  • Wright CM, Majumdar A, Tolman JR, Ostermeier M (2010).  NMR chracterization of an engineered domain fusion between maltose binding protein and TEM β-lactamase provides Insight into Its structure and allosteric mechanism.  Proteins: Structure, Function and Bioinformatics.  78(6).  1423-1430.
  • Hida K, Won SY, Di Pasquale G, Hanes J, Chiorini JA, Ostermeier M (2010).  Sites in the AAV5 capsid tolerant to deletions and tandem duplications.  Archives of Biochemistry and Biophysics.  496(1).  1-8.
  • Meister GE, Chandrasegaran S, Ostermeier M (2009).  Heterodimeric DNA methyltransferases as a platform for creating designer zinc finger methyltransferases for targeted DNA methylation in cells.  Nucleic Acids Research.  38(5).  1749-1759.
  • Kim CS, Pierre B, Ostermeier M, Looger LL, Kim JR (2009).  Enzyme stabilization by domain insertion into a thermophilic protein.  Protein Engineering, Design and Selection.  22(10).  615-623.
  • Ostermeier M, Limberg C, Herwig C, Ziemer B (2009).  Stabilizing the boat conformation of piperazines coordinated to iron (II): Iso-butyl substituents lead to robust oxidation catalysts via hyperconjugation.  Zeitschrift fur Anorganische und Allgemeine Chemie.  635(12).  1823-1830.
  • Ostermeier M (2009).  Designing switchable enzymes.  Current Opinion in Structural Biology.  19(4).  442-448.
  • Sohka T, Heins RA, Ostermeier M (2009).  Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter.  Journal of Biological Engineering.  3.
  • Sohka T, Heins RA, Phelan RM, Greisler JM, Townsend CA, Ostermeier M (2009).  An externally tunable bacterial band-pass filter.  Proceedings of the National Academy of Sciences of the United States of America.  106(25).  10135-10140.
  • Phelan RM, Ostermeier M, Townsend CA (2009).  Design and synthesis of a β-lactamase activated 5-fluorouracil prodrug.  Bioorganic and Medicinal Chemistry Letters.  19(4).  1261-1263.
  • Meister GE, Chandrasegaran S, Ostermeier M (2008).  An engineered split M.HhaI-zinc finger fusion lacks the intended methyltransferase specificity.  Biochemical and Biophysical Research Communications.  377(1).  226-230.
  • Berrondo M, Ostermeier M, Gray JJ (2008).  Structure Prediction of Domain Insertion Proteins from Structures of Individual Domains.  Structure.  16(4).  513-527.
  • Meudtner RM, Ostermeier M, Goddard R, Limberg C, Hecht S (2007).  Multifunctional "clickates" as versatile extended heteroaromatic building blocks: Efficient synthesis via click chemistry, conformational preferences, and metal coordination.  Chemistry - A European Journal.  13(35).  9834-9840.
  • Hida K, Hanes J, Ostermeier M (2007).  Directed evolution for drug and nucleic acid delivery.  Advanced Drug Delivery Reviews.  59(15).  1562-1578.
  • Ostermeier M, Limberg C, Ziemer B, Karunakaran V (2007).  Solvent-dependent oxidation of a (pyridylmethyl)amino ligand by FeCl 3 to give a water-soluble blue fluorophore.  Angewandte Chemie - International Edition.  46(28).  5329-5331.
  • Wright CM, Heins RA, Ostermeier M (2007).  As easy as flipping a switch?.  Current Opinion in Chemical Biology.  11(3).  342-346.
  • Liang J, Jin RK, Boock JT, Mansell TJ, Ostermeier M (2007).  Ligand binding and allostery can emerge simultaneously.  Protein Science.  16(5).  929-937.
  • Ostermeier M (2007).  Beyond cataloging the Library of Babel.  Chem Biol.  14(3).  237-8.
  • Ostermeier M, Limberg C, Ziemer B (2006).  The coordination chemistry of iron with the 1,4-bis(2-pyridyl-methyl) piperazine ligand.  Zeitschrift fur Anorganische und Allgemeine Chemie.  632(7).  1287-1292.
  • Durai S, Bosley A, Abulencia AB, Chandrasegaran S, Ostermeier M (2006).  A bacterial one-hybrid selection system for interrogating zinc finger-DNA interactions.  Combinatorial Chemistry and High Throughput Screening.  9(4).  301-311.
  • Kim JR, Ostermeier M (2006).  Modulation of effector affinity by hinge region mutations also modulates switching activity in an engineered allosteric TEM1 β-lactamase switch.  Archives of Biochemistry and Biophysics.  446(1).  44-51.
  • Guntas G, Liang J, Kim JR, Mansell TJ, Boock J, Ostermeier M (2005).  Protein switches created by non-homologous recombination.  AIChE Annual Meeting, Conference Proceedings.  8054.
  • Paschon DE, Patel ZS, Ostermeier M (2005).  Enhanced catalytic efficiency of aminoglycoside phosphotransferase (3′)-IIa achieved through protein fragmentation and reassembly.  Journal of Molecular Biology.  353(1).  26-37.
  • Choe W, Chandrasegaran S, Ostermeier M (2005).  Protein fragment complementation in M.HhaI DNA methyltransferase.  Biochemical and Biophysical Research Communications.  334(4).  1233-1240.
  • Guntas G, Mansell TJ, Kim JR, Ostermeier M (2005).  Directed evolution of protein switches and their application to the creation of ligand-binding proteins.  Proceedings of the National Academy of Sciences of the United States of America.  102(32).  11224-11229.
  • Ostermeier M (2005).  Engineering allosteric protein switches by domain insertion.  Protein Engineering, Design and Selection.  18(8).  359-364.
  • Bosley AD, Ostermeier M (2005).  Mathematical expressions useful in the construction, description and evaluation of protein libraries.  Biomolecular Engineering.  22(1-3).  57-61.
  • Guntas G, Mitchell SF, Ostermeier M (2004).  A molecular switch created by in vitro recombination of nonhomologous genes.  Chemistry and Biology.  11(11).  1483-1487.
  • Paschon DE, Ostermeier M (2004).  Construction of protein fragment complementation libraries using incremental truncation.  Methods in Enzymology.  388.  103-116.
  • Guntas G, Ostermeier M (2004).  Creation of an Allosteric Enzyme by Domain Insertion.  Journal of Molecular Biology.  336(1).  263-273.
  • Ostermeier M (2003).  Theoretical distribution of truncation lengths in incremental truncation libraries.  Biotechnology and Bioengineering.  82(5).  564-577.
  • Ostermeier M (2003).  Synthetic gene libraries: In search of the optimal diversity.  Trends in Biotechnology.  21(6).  244-247.
  • Lutz S, Ostermeier M (2003).  Preparation of SCRATCHY hybrid protein libraries: size- and in-frame selection of nucleic acid sequences.  Methods Mol Biol.  231.  143-51.
  • Ostermeier M, Lutz S (2003).  The creation of ITCHY hybrid protein libraries.  Methods Mol Biol.  231.  129-41.
  • Lutz S, Ostermeier M, Moore GL, Maranas CD, Benkovic SJ (2001).  Creating multiple-crossover DNA libraries independent of sequence identity.  Proceedings of the National Academy of Sciences of the United States of America.  98(20).  11248-11253.
  • Ostermeier M, Benkovic SJ (2001).  Construction of hybrid gene libraries involving the circular permutation of DNA.  Biotechnology Letters.  23(4).  303-310.
  • Lutz S, Ostermeier M, Benkovic SJ (2001).  Rapid generation of incremental truncation libraries for protein engineering using alpha-phosphothioate nucleotides..  Nucleic acids research.  29(4).
  • Ostermeier M, Benkovic SJ (2000).  Evolution of protein function by domain swapping.  Advances in Protein Chemistry.  55.  29-78.
  • Ostermeier M, Benkovic SJ (2000).  A two-phagemid system for the creation of non-phage displayed antibody libraries approaching one trillion members.  Journal of Immunological Methods.  237(1-2).  175-186.
  • Ostermeier M, Nixon AE, Shim JH, Benkovic SJ (1999).  Combinatorial protein engineering by incremental truncation.  Proceedings of the National Academy of Sciences of the United States of America.  96(7).  3562-3567.
  • Benkovic SJ, Ostermeier M (1999).  Finding Cinderella's slipper-proteins that fit.  Nat Biotechnol.  17(7).  639-40.
  • Ostermeier M, Shim JH, Benkovic SJ (1999).  A combinatorial approach to hybrid enzymes independent of DNA homology.  Nature Biotechnology.  17(12).  1205-1209.
  • Ostermeier M, Nixon AE, Benkovic SJ (1999).  Incremental truncation as a strategy in the engineering of novel biocatalysts.  Bioorganic and Medicinal Chemistry.  7(10).  2139-2144.
  • Nixon AE, Ostermeier M, Benkovic SJ (1998).  Hybrid enzymes: Manipulating enzyme design.  Trends in Biotechnology.  16(6).  258-264.
  • Ostermeier M, De Sutter K, Georgiou G (1996).  Eukaryotic protein disulfide isomerase complements Escherichia coli dsbA mutants and increases the yield of a heterologous secreted protein with disulfide bonds.  Journal of Biological Chemistry.  271(18).  10616-10622.
  • Ostermeier M, Georgiou G (1994).  The folding of bovine pancreatic trypsin inhibitor in the Escherichia coli periplasm.  Journal of Biological Chemistry.  269(33).  21072-21077.
  • Georgiou G, Valax P, Ostermeier M, Horowitz PM (1994).  Folding and aggregation of TEM β‐lactamase: Analogies with the formation of inclusion bodies in Escherichia coli.  Protein Science.  3(11).  1953-1960.
Book Chapters
  • Ribeiro LF, Warren TD, Ostermeier M (2017).  Construction of protein switches by domain insertion and directed evolution.  Methods in Molecular Biology.  1596.  43-55.
  • Kanwar M, Wright RC, Date A, Tullman J, Ostermeier M (2013).  Protein switch engineering by domain insertion.  Methods in Enzymology.  523.  369-388.
  • Meister GE, Kanwar M, Ostermeier M (2011).  Circular Permutation of Proteins.  Protein Engineering Handbook, Volume 1 & Volume 2.  2.  453-471.
  • Meister G, Kanwar M, Ostermeier M (2009).  Circular permutation of proteins.  Protein Engineering Handbook.  Wiley.
  • Ostermeier M, Lutz S, Benkovic S (2002).  Generation of protein fragment libraries by incremental truncation..  Protein-Protein Interactions: A Molecular Cloning Manual.  Cold Spring Harbor Laboratory Press.
Patents
  • Firnberg E, Ostermeier M  "Methods for efficient, expansive, user-defined DNA mutagenesis", 2017.
  • Firnberg E, Ostermeier M  "Methods for efficient, expansive, user-defined DNA mutagenesis", 2016.
  • Ostermeier M, Wright CM  "Prodrug activation in cancer cells using molecular switches", 2016.
  • Firnberg E, Ostermeier M  "Methods for efficient, expansive user-defined DNA mutagenesis", 2016.
  • Guntas G, Ostermeier M  "Methods for making and using molecular switches involving circular permutation", 2016.
  • Ostermeier M  "Molecular switches and methods for making and using the same", 2016.
  • Meister G, Novina C, Ostermeier M, Xiong T  "Systems and methods for genome modification and regulation", 2015.
  • Ostermeier M, Wright CM  "Prodrug activation in cancer cells using molecular switches", 2014.
  • Ostermeier M  "Methods for making and using molecular switches involving circular permutation", 2014.
  • Kim C, Kim JR, Ostermeier M, Pierre B  "Protein stabilization by domain insertion into a thermophilic protein", 2013.
  • Ostermeier M  "Molecular switches and methods for making and using the same", 2013.
  • Guntas G, Ostermeier M  "Methods for making and using molecular switches involving circular permutation", 2012.
  • Benkovic SJ, Lutz S, Nixon A, Ostermeier M  "Incrementally truncated nucleic acids and methods of making same", 2010.
  • Benkovic SJ, Lutz S, Nixon A, Ostermeier M  "Incrementally truncated nucleic acids and methods of making same", 2008.
  • Georgiou G, Ostermeier M  "Methods for producing soluble, biologically-active disulfide-bond containing eukaryotic proteins in bacterial cells", 2000.
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