Tanja Kortemme, PhD

Title(s)Professor, Bioengineering
SchoolSchool of Pharmacy
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    Collapse Biography 
    Collapse Awards and Honors
    Chan Zuckerberg Biohub2017Investigator
    W.M. Keck Foundation2013Medical Research Award
    Gen920121st Place, G-Prize
    National Science Foundation (NSF)2008CAREER Award
    Alfred P. Sloan Foundation2005Junior Faculty Award
    Human Frontiers Science Program (HFSP)2000Postdoctoral Fellow
    European Molecular Biology Organization (EMBO)1999Postdoctoral Fellow
    European Molecular Biology Laboratory (EMBL)1993Graduate Fellow
    German National Academic Foundation ("Studienstiftung des Deutschen Volkes")1989Scholar

    Collapse Overview 
    Collapse Overview
    Engineered biological systems, ranging from molecules with new functions to entire organisms, have tremendous practical importance; they can also fundamentally change how we ask questions about the biological principles of function and fitness. Our research aims to invent approaches to engineer new molecules that operate as predicted in biological contexts, and to utilize prediction and engineering to address fundamental questions on the relationship of molecular characteristics, cellular function and organismal fitness. To address the many current challenges in the field – from developing more predictive computational design methods to determining the requirements for function in cells – we combine concepts from computer science, physics, chemistry, mathematics, engineering and biology.

    Our work spans three interrelated themes:

    I. Develop computational methods for modeling & design of proteins, in the program Rosetta (www.rosettacommons.org).

    Predicting and designing the structures of proteins with biologically useful accuracy has been a key challenge in computational structural biology and molecular engineering. We have made methodological advances that address one of the main bottlenecks: sampling the vast number of conformations accessible to proteins. We have utilized a method for moving through conformational space inspired by principles from robotics – a field with a rich history in efficient calculation of mechanically accessible states subject to constraints. We applied the same mathematics that can be used to direct the motions of a robot arm to compute the degrees of freedom of a polypeptide chain (Mandell et al., Nature Methods 2009). Our predictions generate hypotheses on protein conformations controlling biological processes – such as protein recognition, signal transduction, and enzyme active site gating – and are laying the foundation for our work reengineering and “reshaping” protein interfaces and active sites for new functions.

    II. Create new proteins and devices with more advanced functions by experimental engineering.

    Designer molecules with new biological functions could have many exciting uses: protein therapeutics with minimal side effects; new enzymes and biological synthesis pathways for fuel molecules or compounds that are otherwise too expensive to produce; sensor/actuator devices that can report on cell biological processes in real time; robust signaling systems that can detect specific inputs and generate a precise response; protein machines that can be controlled by specific external inputs such as light. Over the past several years, we have engineered a range of proteins with new functions, including protein-protein interactions that are specific enough to control complex biological processes in mammalian cells (Kapp et al., PNAS, 2012). We have also engineered proteins whose functions can be switched by phosphorylation or light. A recent highlight is a study describing the control of precise shape transitions of a large protein assembly with optical inputs, where we successfully exchanged the ‘engine’ of a protein-based ATP-driven molecular machine to be powered by light (Hoersch et al., Nature Nanotechnology 2013). A current focus is to apply computational protein design to create new proteins that can sense molecular signals in living cells and orchestrate desired biological responses.

    III. Dissect design principles of function in cells by combining prediction and engineering approaches.

    Cells must balance the cost and benefit to optimize organismal fitness. In a recent study, we used the lac operon of Escherichia coli – a classic system for regulatory mechanisms that balance cost and benefit of protein expression – to quantify the economics of protein production (Eames & Kortemme, Science 2012). A current experimental effort is directed towards determining the system-level functions of specific interactions in cells and organisms by systematically modulating protein interactions and protein abundance. In a new project, we have begun to characterize large-scale genetic interactions of engineered proteins with altered interaction patterns, using the E-MAP (epistatic mini array profile) technology, in collaboration with Nevan Krogan’s laboratory at UCSF. With Mark von Zastrow's group at UCSF, we have reengineered and characterized PDZ-domain mediated interactions in the recycling of G-protein coupled receptors to quantify the interaction specificities of protein-peptide interactions in the context of cellular processes. These investigations reveal an unexpected functional promiscuity in cellular networks, and suggest that there are biologically important differences between biochemically possible and functionally utilized interactions.

    Collapse Research 
    Collapse Research Activities and Funding
    Computational design of Cas9-based molecular imaging reagents
    NIH/NIBIB R21EB021453May 10, 2016 - Feb 28, 2018
    Role: Principal Investigator
    Discovery of Protein Network Function
    NIH/NIGMS R01GM117189Jan 1, 2016 - Dec 31, 2019
    Role: Principal Investigator
    Computational design of protein-based small-molecule biosensors
    NIH/NIGMS R01GM110089May 1, 2015 - Apr 30, 2019
    Role: Principal Investigator
    Integrating computation and genetics to quantify specificity in protein networks
    NIH/NIGMS R01GM098101Aug 1, 2011 - May 31, 2015
    Role: Co-Principal Investigator
    Computational design of protein-based modular small-molecule biosensors
    NIH/NIBIB R21EB013389Apr 1, 2011 - Mar 31, 2014
    Role: Principal Investigator
    Molecular Biophysics Training Grant
    NIH/NIGMS T32GM008284Sep 30, 1988 - Jun 30, 2023
    Role: Co-Principal Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
    Collapse Websites

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun. 2019 05 09; 10(1):2127. PMID: 31073154.
      View in: PubMed
    2. Kundert K, Kortemme T. Computational design of structured loops for new protein functions. Biol Chem. 2019 Jan 24. PMID: 30676995.
      View in: PubMed
    3. Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open. 2018 Jul 23; 7(7). PMID: 30037883.
      View in: PubMed
    4. Barlow KA, Ó Conchúir S, Thompson S, Suresh P, Lucas JE, Heinonen M, Kortemme T. Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. J Phys Chem B. 2018 May 31; 122(21):5389-5399. PMID: 29401388.
      View in: PubMed
    5. Smart AD, Pache RA, Thomsen ND, Kortemme T, Davis GW, Wells JA. Engineering a light-activated caspase-3 for precise ablation of neurons in vivo. Proc Natl Acad Sci U S A. 2017 09 26; 114(39):E8174-E8183. PMID: 28893998.
      View in: PubMed
    6. Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J. Deconstruction of the Ras switching cycle through saturation mutagenesis. Elife. 2017 07 07; 6. PMID: 28686159.
      View in: PubMed
    7. Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. J Chem Theory Comput. 2017 Jun 13; 13(6):3031-3048. PMID: 28430426.
      View in: PubMed
    8. Mavor D, Barlow K, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate RE, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo EC, See SK, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. Elife. 2016 04 25; 5. PMID: 27111525; PMCID: PMC4862753.
    9. Hoersch D, Kortemme T. A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine. Structure. 2016 Apr 05; 24(4):576-584. PMID: 27021162.
      View in: PubMed
    10. Ritterson RS, Hoersch D, Barlow KA, Kortemme T. Design of Light-Controlled Protein Conformations and Functions. Methods Mol Biol. 2016; 1414:197-211. PMID: 27094293.
      View in: PubMed
    11. Ollikainen N, de Jong RM, Kortemme T. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity. PLoS Comput Biol. 2015; 11(9):e1004335. PMID: 26397464; PMCID: PMC4580623.
    12. Ó Conchúir S, Barlow KA, Pache RA, Ollikainen N, Kundert K, O'Meara MJ, Smith CA, Kortemme T. A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. PLoS One. 2015; 10(9):e0130433. PMID: 26335248.
      View in: PubMed
    13. O'Meara MJ, Leaver-Fay A, Tyka MD, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B. Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. J Chem Theory Comput. 2015 Feb 10; 11(2):609-22. PMID: 25866491.
      View in: PubMed
    14. Melero C, Ollikainen N, Harwood I, Karpiak J, Kortemme T. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):15426-31. PMID: 25313039; PMCID: PMC4217408.
    15. Koide S, Kortemme T. Editorial overview: Engineering and design: raising the bar through innovation and integration. Curr Opin Struct Biol. 2014 Aug; 27:vi-viii. PMID: 25175941.
      View in: PubMed
    16. Hoersch D, Roh SH, Chiu W, Kortemme T. Reprogramming an ATP-driven protein machine into a light-gated nanocage. Nat Nanotechnol. 2013 Dec; 8(12):928-32. PMID: 24270642; PMCID: PMC3859876.
    17. Ollikainen N, Kortemme T. Computational protein design quantifies structural constraints on amino acid covariation. PLoS Comput Biol. 2013; 9(11):e1003313. PMID: 24244128; PMCID: PMC3828131.
    18. Jackson EL, Ollikainen N, Covert AW, Kortemme T, Wilke CO. Amino-acid site variability among natural and designed proteins. PeerJ. 2013; 1:e211. PMID: 24255821; PMCID: PMC3828621.
    19. Ritterson RS, Kuchenbecker KM, Michalik M, Kortemme T. Design of a photoswitchable cadherin. J Am Chem Soc. 2013 Aug 28; 135(34):12516-9. PMID: 23923816; PMCID: PMC3774674.
    20. Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PLoS One. 2013; 8(5):e63906. PMID: 23717507; PMCID: PMC3661552.
    21. Stein A, Kortemme T. Improvements to robotics-inspired conformational sampling in rosetta. PLoS One. 2013; 8(5):e63090. PMID: 23704889; PMCID: PMC3660577.
    22. Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, Baker D, Kuhlman B. Scientific benchmarks for guiding macromolecular energy function improvement. Methods Enzymol. 2013; 523:109-43. PMID: 23422428; PMCID: PMC3724755.
    23. Ollikainen N, Smith CA, Fraser JS, Kortemme T. Flexible backbone sampling methods to model and design protein alternative conformations. Methods Enzymol. 2013; 523:61-85. PMID: 23422426; PMCID: PMC3750959.
    24. Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJS, Jacobson MP, Kortemme T. Design of a phosphorylatable PDZ domain with peptide-specific affinity changes. Structure. 2013 Jan 08; 21(1):54-64. PMID: 23159126.
      View in: PubMed
    25. Humphris-Narayanan E, Akiva E, Varela R, Ó Conchúir S, Kortemme T. Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design. PLoS Comput Biol. 2012; 8(8):e1002639. PMID: 22927804; PMCID: PMC3426558.
    26. Eames M, Kortemme T. Cost-benefit tradeoffs in engineered lac operons. Science. 2012 May 18; 336(6083):911-5. PMID: 22605776.
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    27. Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T. Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci U S A. 2012 Apr 03; 109(14):5277-82. PMID: 22403064; PMCID: PMC3325720.
    28. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70. PMID: 22190034; PMCID: PMC3310911.
    29. Chao LH, Stratton MM, Lee IH, Rosenberg OS, Levitz J, Mandell DJ, Kortemme T, Groves JT, Schulman H, Kuriyan J. A mechanism for tunable autoinhibition in the structure of a human Ca2+/calmodulin- dependent kinase II holoenzyme. Cell. 2011 Sep 02; 146(5):732-45. PMID: 21884935; PMCID: PMC3184253.
    30. Smith CA, Kortemme T. Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design. PLoS One. 2011; 6(7):e20451. PMID: 21789164; PMCID: PMC3138746.
    31. Babor M, Mandell DJ, Kortemme T. Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface. Protein Sci. 2011 Jun; 20(6):1082-9. PMID: 21465611; PMCID: PMC3104238.
    32. Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popovic Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 2011; 487:545-74. PMID: 21187238; PMCID: PMC4083816.
    33. Moon TS, Clarke EJ, Groban ES, Tamsir A, Clark RM, Eames M, Kortemme T, Voigt CA. Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. J Mol Biol. 2011 Feb 18; 406(2):215-27. PMID: 21185306; PMCID: PMC3033806.
    34. Lauffer BE, Melero C, Temkin P, Lei C, Hong W, Kortemme T, von Zastrow M. SNX27 mediates PDZ-directed sorting from endosomes to the plasma membrane. J Cell Biol. 2010 Aug 23; 190(4):565-74. PMID: 20733053; PMCID: PMC2928020.
    35. Smith CA, Kortemme T. Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains. J Mol Biol. 2010 Sep 17; 402(2):460-74. PMID: 20654621.
      View in: PubMed
    36. Lauck F, Smith CA, Friedland GF, Humphris EL, Kortemme T. RosettaBackrub--a web server for flexible backbone protein structure modeling and design. Nucleic Acids Res. 2010 Jul; 38(Web Server issue):W569-75. PMID: 20462859; PMCID: PMC2896185.
    37. Friedland GD, Kortemme T. Designing ensembles in conformational and sequence space to characterize and engineer proteins. Curr Opin Struct Biol. 2010 Jun; 20(3):377-84. PMID: 20303740.
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    38. Mandell DJ, Kortemme T. Computer-aided design of functional protein interactions. Nat Chem Biol. 2009 Nov; 5(11):797-807. PMID: 19841629.
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    39. Mandell DJ, Kortemme T. Backbone flexibility in computational protein design. Curr Opin Biotechnol. 2009 Aug; 20(4):420-8. PMID: 19709874.
      View in: PubMed
    40. Mandell DJ, Coutsias EA, Kortemme T. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 2009 Aug; 6(8):551-2. PMID: 19644455; PMCID: PMC2847683.
    41. Babor M, Kortemme T. Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility. Proteins. 2009 Jun; 75(4):846-58. PMID: 19194863; PMCID: PMC3978785.
    42. Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol. 2009 May; 5(5):e1000393. PMID: 19478996; PMCID: PMC2682763.
    43. Oberdorf R, Kortemme T. Complex topology rather than complex membership is a determinant of protein dosage sensitivity. Mol Syst Biol. 2009; 5:253. PMID: 19293832.
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    44. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9. PMID: 19217386; PMCID: PMC2739730.
    45. Freedman TS, Sondermann H, Kuchment O, Friedland GD, Kortemme T, Kuriyan J. Differences in flexibility underlie functional differences in the Ras activators son of sevenless and Ras guanine nucleotide releasing factor 1. Structure. 2009 Jan 14; 17(1):41-53. PMID: 19141281; PMCID: PMC2654222.
    46. Ollikainen N, Sentovich E, Coelho C, Kuehlmann A, Kortemme T.SAT-based Protein Design. 2009 IEEE/ACM International Conference on Computer-Aided Design Digest of Technical Papers (ICCAD 2009). 2009; 128-35.
    47. Humphris EL, Kortemme T. Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design. Structure. 2008 Dec 10; 16(12):1777-88. PMID: 19081054.
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    48. Lauffer BE, Chen S, Melero C, Kortemme T, von Zastrow M, Vargas GA. Engineered protein connectivity to actin mimics PDZ-dependent recycling of G protein-coupled receptors but not its regulation by Hrs. J Biol Chem. 2009 Jan 23; 284(4):2448-58. PMID: 19001361; PMCID: PMC2629119.
    49. Smith CA, Kortemme T. Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol. 2008 Jul 18; 380(4):742-56. PMID: 18547585; PMCID: PMC2603262.
    50. Friedland GD, Linares AJ, Smith CA, Kortemme T. A simple model of backbone flexibility improves modeling of side-chain conformational variability. J Mol Biol. 2008 Jul 18; 380(4):757-74. PMID: 18547586; PMCID: PMC3574579.
    51. McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK. A new twist in TCR diversity revealed by a forbidden alphabeta TCR. J Mol Biol. 2008 Feb 01; 375(5):1306-19. PMID: 18155234; PMCID: PMC2330282.
    52. Eames M, Kortemme T. Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance. Structure. 2007 Nov; 15(11):1442-51. PMID: 17997970; PMCID: PMC2600897.
    53. Lengyel CS, Willis LJ, Mann P, Baker D, Kortemme T, Strong RK, McFarland BJ. Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity. J Biol Chem. 2007 Oct 19; 282(42):30658-66. PMID: 17690100.
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    54. Humphris EL, Kortemme T. Design of multi-specificity in protein interfaces. PLoS Comput Biol. 2007 Aug; 3(8):e164. PMID: 17722975; PMCID: PMC1950952.
    55. Freedman TS, Sondermann H, Friedland GD, Kortemme T, Bar-Sagi D, Marqusee S, Kuriyan J. A Ras-induced conformational switch in the Ras activator Son of sevenless. Proc Natl Acad Sci U S A. 2006 Nov 07; 103(45):16692-7. PMID: 17075039.
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    56. Wang SX, Pandey KC, Somoza JR, Sijwali PS, Kortemme T, Brinen LS, Fletterick RJ, Rosenthal PJ, McKerrow JH. Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease. Proc Natl Acad Sci U S A. 2006 Aug 01; 103(31):11503-8. PMID: 16864794.
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    57. Joachimiak LA, Kortemme T, Stoddard BL, Baker D. Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J Mol Biol. 2006 Aug 04; 361(1):195-208. PMID: 16831445.
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    58. Palmer AE, Giacomello M, Kortemme T, Hires SA, Lev-Ram V, Baker D, Tsien RY. Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chem Biol. 2006 May; 13(5):521-30. PMID: 16720273.
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    59. Song G, Lazar GA, Kortemme T, Shimaoka M, Desjarlais JR, Baker D, Springer TA. Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. J Biol Chem. 2006 Feb 24; 281(8):5042-9. PMID: 16354667; PMCID: PMC1455478.
    60. Jiang L, Kuhlman B, Kortemme T, Baker D. A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins. 2005 Mar 01; 58(4):893-904. PMID: 15651050.
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    61. Morozov AV, Kortemme T. Potential functions for hydrogen bonds in protein structure prediction and design. Adv Protein Chem. 2005; 72:1-38. PMID: 16581371.
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    62. Chen Y, Kortemme T, Robertson T, Baker D, Varani G. A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res. 2004; 32(17):5147-62. PMID: 15459285; PMCID: PMC521638.
    63. Morozov AV, Kortemme T, Tsemekhman K, Baker D. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci U S A. 2004 May 04; 101(18):6946-51. PMID: 15118103.
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    64. Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D. Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol. 2004 Apr; 11(4):371-9. PMID: 15034550.
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    65. Svensson HG, Wedemeyer WJ, Ekstrom JL, Callender DR, Kortemme T, Kim DE, Sjöbring U, Baker D. Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain. Biochemistry. 2004 Mar 09; 43(9):2445-57. PMID: 14992582.
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    66. Kortemme T, Kim DE, Baker D. Computational alanine scanning of protein-protein interfaces. Sci STKE. 2004 Feb 03; 2004(219):pl2. PMID: 14872095.
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    67. Kortemme T, Baker D. Computational design of protein-protein interactions. Curr Opin Chem Biol. 2004 Feb; 8(1):91-7. PMID: 15036162.
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    68. Morozov AV, Kortemme T, Baker D.Evaluation of Models of Electrostatic Interactions in Proteins. J. Phys. Chem. B. 2003; 107:2075-90.
    69. Boulanger MJ, Bankovich AJ, Kortemme T, Baker D, Garcia KC. Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130. Mol Cell. 2003 Sep; 12(3):577-89. PMID: 14527405.
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    70. Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D. Protein-protein docking predictions for the CAPRI experiment. Proteins. 2003 Jul 01; 52(1):118-22. PMID: 12784377.
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    71. McFarland BJ, Kortemme T, Yu SF, Baker D, Strong RK. Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands. Structure. 2003 Apr; 11(4):411-22. PMID: 12679019.
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    72. Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol. 2003 Feb 28; 326(4):1239-59. PMID: 12589766.
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    73. Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci U S A. 2002 Oct 29; 99(22):14116-21. PMID: 12381794; PMCID: PMC137846.
    74. Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL. Design, activity, and structure of a highly specific artificial endonuclease. Mol Cell. 2002 Oct; 10(4):895-905. PMID: 12419232.
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    75. Alm E, Morozov AV, Kortemme T, Baker D. Simple physical models connect theory and experiment in protein folding kinetics. J Mol Biol. 2002 Sep 13; 322(2):463-76. PMID: 12217703.
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    76. Kortemme T, Kelly MJ, Kay LE, Forman-Kay J, Serrano L. Similarities between the spectrin SH3 domain denatured state and its folding transition state. J Mol Biol. 2000 Apr 14; 297(5):1217-29. PMID: 10764585.
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    77. Lacroix E, Kortemme T, Lopez de la Paz M, Serrano L. The design of linear peptides that fold as monomeric beta-sheet structures. Curr Opin Struct Biol. 1999 Aug; 9(4):487-93. PMID: 10449370.
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    78. Ramírez-Alvarado M, Kortemme T, Blanco FJ, Serrano L. Beta-hairpin and beta-sheet formation in designed linear peptides. Bioorg Med Chem. 1999 Jan; 7(1):93-103. PMID: 10199660.
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    79. Kortemme T, Ramírez-Alvarado M, Serrano L. Design of a 20-amino acid, three-stranded beta-sheet protein. Science. 1998 Jul 10; 281(5374):253-6. PMID: 9657719.
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    80. Bulaj G, Kortemme T, Goldenberg DP. Ionization-reactivity relationships for cysteine thiols in polypeptides. Biochemistry. 1998 Jun 23; 37(25):8965-72. PMID: 9636038.
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    81. Kortemme T, Darby NJ, Creighton TE. Electrostatic interactions in the active site of the N-terminal thioredoxin-like domain of protein disulfide isomerase. Biochemistry. 1996 Nov 19; 35(46):14503-11. PMID: 8931546.
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    82. Kortemme T, Hollecker M, Kemmink J, Creighton TE. Comparison of the (30-51, 14-38) two-disulphide folding intermediates of the homologous proteins dendrotoxin K and bovine pancreatic trypsin inhibitor by two-dimensional 1H nuclear magnetic resonance. J Mol Biol. 1996 Mar 22; 257(1):188-98. PMID: 8632454.
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    83. Kortemme T, Creighton TE. Ionisation of cysteine residues at the termini of model alpha-helical peptides. Relevance to unusual thiol pKa values in proteins of the thioredoxin family. J Mol Biol. 1995 Nov 10; 253(5):799-812. PMID: 7473753.
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    84. Chakrabartty A, Kortemme T, Baldwin RL. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 1994 May; 3(5):843-52. PMID: 8061613; PMCID: PMC2142718.
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