Anthony Kossiakoff

Research Summary
The Kossiakoff Group's research interests are to provide a molecular understanding of how molecular recognition governs virtually all aspects of biological function. To study these issues our group employs a combination of X-ray crystallography and cryo-EM, site-directed mutagenesis, phage display and biophysical analysis. The Kossiakoff group has also pioneered a new technology called “chaperone-assisted” crystallography, which has facilitated the structural analyses of protein systems that had been totally recalcitrant to other approaches. The group has also been at the forefront of developing synthetic antibodies. These synthetic antibodies are much more powerful that traditional monoclonal antibodies and have the potential to completely replace them for uses in live cell imaging and proteomics.
Protein Engineering, Structural Biology, Phage Display Mutagenesis, Antibody Engineering, T-cell Engineering, Membrane Proteins
  • Davis and Elkins College, BS Chemistry/Math 09/1968
  • University of Delaware, Ph.D Physical Chemistry 09/1972
  • California Institute of Technology, Postdoc Structural Biology 05/1975
Biosciences Graduate Program Association
Awards & Honors
  • 1983 - 1998 Director Department of Protein Engineering Genentech, Inc.
  • 1998 - 2003 Director Institute for Biophysical Dynamics University of Chicago
  • 1998 - 2011 Chair Department of Biochemistry and Molecular Biology University of Chicago
  • 2003 - Alumni Hall of Fame University of Delaware
  • 2011 - Honorary Degree Doctor of Science Davis and Elkins College
  • 2012 - Fellow of American Association for Advancement of Science AAAS
  • 2019 - Christian Anfinsen Award Protein Society
  1. Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder. Nat Commun. 2023 02 06; 14(1):635. View in: PubMed

  2. Structure, sequon recognition and mechanism of tryptophan C-mannosyltransferase. Nat Chem Biol. 2023 May; 19(5):575-584. View in: PubMed

  3. Development, structure, and mechanism of synthetic antibodies that target claudin and Clostridium perfringens enterotoxin complexes. J Biol Chem. 2022 09; 298(9):102357. View in: PubMed

  4. Structures of atypical chemokine receptor 3 reveal the basis for its promiscuity and signaling bias. Sci Adv. 2022 07 15; 8(28):eabn8063. View in: PubMed

  5. A peroxisomal ubiquitin ligase complex forms a retrotranslocation channel. Nature. 2022 07; 607(7918):374-380. View in: PubMed

  6. Structure of human NTCP reveals the basis of recognition and sodium-driven transport of bile salts into the liver. Cell Res. 2022 08; 32(8):773-776. View in: PubMed

  7. Architecture of the cytoplasmic face of the nuclear pore. Science. 2022 06 10; 376(6598):eabm9129. View in: PubMed

  8. Quaternary structure independent folding of voltage-gated ion channel pore domain subunits. Nat Struct Mol Biol. 2022 06; 29(6):537-548. View in: PubMed

  9. Synthetic Antibodies Detect Distinct Cellular States of Chromosome Passenger Complex Proteins. J Mol Biol. 2022 06 30; 434(12):167602. View in: PubMed

  10. Structural basis of lipopolysaccharide maturation by the O-antigen ligase. Nature. 2022 04; 604(7905):371-376. View in: PubMed

  11. Engineering of a synthetic antibody fragment for structural and functional studies of K+ channels. J Gen Physiol. 2022 04 04; 154(4). View in: PubMed

  12. Targeting a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) for RAS-driven cancers. J Clin Invest. 2022 02 15; 132(4). View in: PubMed

  13. Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins. Proc Natl Acad Sci U S A. 2021 11 23; 118(47). View in: PubMed

  14. Structure of an AMPK complex in an inactive, ATP-bound state. Science. 2021 07 23; 373(6553):413-419. View in: PubMed

  15. Structures of ABCB4 provide insight into phosphatidylcholine translocation. Proc Natl Acad Sci U S A. 2021 08 17; 118(33). View in: PubMed

  16. Structures of rhodopsin in complex with G-protein-coupled receptor kinase 1. Nature. 2021 07; 595(7868):600-605. View in: PubMed

  17. K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle. Nat Chem Biol. 2021 08; 17(8):896-905. View in: PubMed

  18. A T cell redirection platform for co-targeting dual antigens on solid tumors. MAbs. 2021 Jan-Dec; 13(1):1933690. View in: PubMed

  19. Structural basis of omega-3 fatty acid transport across the blood-brain barrier. Nature. 2021 07; 595(7866):315-319. View in: PubMed

  20. Inhibition of Cancer Cell Adhesion, Migration and Proliferation by a Bispecific Antibody that Targets two Distinct Epitopes on av Integrins. J Mol Biol. 2021 07 23; 433(15):167090. View in: PubMed

  21. Engineered Ultra-High Affinity Synthetic Antibodies for SARS-CoV-2 Neutralization and Detection. J Mol Biol. 2021 05 14; 433(10):166956. View in: PubMed

  22. Recognition of an a-helical hairpin in P22 large terminase by a synthetic antibody fragment. Acta Crystallogr D Struct Biol. 2020 Sep 01; 76(Pt 9):876-888. View in: PubMed

  23. Structure of human Frizzled5 by fiducial-assisted cryo-EM supports a heterodimeric mechanism of canonical Wnt signaling. Elife. 2020 08 07; 9. View in: PubMed

  24. Synthetic antibodies against BRIL as universal fiducial marks for single-particle cryoEM structure determination of membrane proteins. Nat Commun. 2020 03 27; 11(1):1598. View in: PubMed

  25. Structure and mechanism of the ER-based glucosyltransferase ALG6. Nature. 2020 03; 579(7799):443-447. View in: PubMed

  26. Structure and drug resistance of the Plasmodium falciparum transporter PfCRT. Nature. 2019 12; 576(7786):315-320. View in: PubMed

  27. Development of "Plug and Play" Fiducial Marks for Structural Studies of GPCR Signaling Complexes by Single-Particle Cryo-EM. Structure. 2019 12 03; 27(12):1862-1874.e7. View in: PubMed

  28. An engineered ultra-high affinity Fab-Protein G pair enables a modular antibody platform with multifunctional capability. Protein Sci. 2020 01; 29(1):141-156. View in: PubMed

  29. Rapid Discovery and Characterization of Synthetic Neutralizing Antibodies against Anthrax Edema Toxin. Biochemistry. 2019 07 09; 58(27):2996-3004. View in: PubMed

  30. Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2. Proc Natl Acad Sci U S A. 2018 10 02; 115(40):10010-10015. View in: PubMed

  31. Structural basis for activation of voltage sensor domains in an ion channel TPC1. Proc Natl Acad Sci U S A. 2018 09 25; 115(39):E9095-E9104. View in: PubMed

  32. The structure of the C-terminal domain of the nucleoprotein from the Bundibugyo strain of the Ebola virus in complex with a pan-specific synthetic Fab. Acta Crystallogr D Struct Biol. 2018 07 01; 74(Pt 7):681-689. View in: PubMed

  33. Publisher Correction: Cryo-EM structure of human rhodopsin bound to an inhibitory G protein. Nature. 2018 09; 561(7724):E44. View in: PubMed

  34. Cryo-EM structure of human rhodopsin bound to an inhibitory G protein. Nature. 2018 06; 558(7711):553-558. View in: PubMed

  35. Reply to Kang and Brooks: Comment on the calculations in protein thermodynamics. J Biol Chem. 2018 04 06; 293(14):5063. View in: PubMed

  36. Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme. Elife. 2018 03 29; 7. View in: PubMed

  37. Engineered synthetic antibodies as probes to quantify the energetic contributions of ligand binding to conformational changes in proteins. J Biol Chem. 2018 02 23; 293(8):2815-2828. View in: PubMed

  38. Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination. J Mol Biol. 2018 02 02; 430(3):337-347. View in: PubMed

  39. Targeted rescue of cancer-associated IDH1 mutant activity using an engineered synthetic antibody. Sci Rep. 2017 04 03; 7(1):556. View in: PubMed

  40. Generating Conformation and Complex-Specific Synthetic Antibodies. Methods Mol Biol. 2017; 1575:93-119. View in: PubMed

  41. Prolactin Receptor-Mediated Internalization of Imaging Agents Detects Epithelial Ovarian Cancer with Enhanced Sensitivity and Specificity. Cancer Res. 2017 04 01; 77(7):1684-1696. View in: PubMed

  42. The Preserved HTH-Docking Cleft of HIV-1 Integrase Is Functionally Critical. Structure. 2016 11 01; 24(11):1936-1946. View in: PubMed

  43. Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment. J Mol Biol. 2016 10 09; 428(20):4100-4114. View in: PubMed

  44. A polar ring endows improved specificity to an antibody fragment. Protein Sci. 2016 07; 25(7):1290-8. View in: PubMed

  45. Conformational Chaperones for Structural Studies of Membrane Proteins Using Antibody Phage Display with Nanodiscs. Structure. 2016 Feb 02; 24(2):300-9. View in: PubMed

  46. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins. PLoS One. 2015; 10(10):e0139695. View in: PubMed

  47. Architecture of the fungal nuclear pore inner ring complex. Science. 2015 Oct 02; 350(6256):56-64. View in: PubMed

  48. A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Mol Cell Proteomics. 2015 Oct; 14(10):2833-47. View in: PubMed

  49. A YidC-like Protein in the Archaeal Plasma Membrane. Structure. 2015 Sep 01; 23(9):1715-1724. View in: PubMed

  50. A New Versatile Immobilization Tag Based on the Ultra High Affinity and Reversibility of the Calmodulin-Calmodulin Binding Peptide Interaction. J Mol Biol. 2015 Aug 14; 427(16):2707-25. View in: PubMed

  51. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat Methods. 2015 Aug; 12(8):725-31. View in: PubMed

  52. Engineering Synthetic Antibody Inhibitors Specific for LD2 or LD4 Motifs of Paxillin. J Mol Biol. 2015 Jul 31; 427(15):2532-2547. View in: PubMed

  53. Phage display selections for affinity reagents to membrane proteins in nanodiscs. Methods Enzymol. 2015; 557:219-45. View in: PubMed

  54. Protein targeting. Structure of the Get3 targeting factor in complex with its membrane protein cargo. Science. 2015 Mar 06; 347(6226):1152-5. View in: PubMed

  55. Nuclear pores. Architecture of the nuclear pore complex coat. Science. 2015 Mar 06; 347(6226):1148-52. View in: PubMed

  56. Scalable high throughput selection from phage-displayed synthetic antibody libraries. J Vis Exp. 2015 Jan 17; (95):51492. View in: PubMed

  57. Engineering synthetic antibody binders for allosteric inhibition of prolactin receptor signaling. Cell Commun Signal. 2015 Jan 15; 13:1. View in: PubMed

  58. Applications for an engineered Protein-G variant with a pH controllable affinity to antibody fragments. J Immunol Methods. 2014 Dec 15; 415:24-30. View in: PubMed

  59. Probing the functions of the paramyxovirus glycoproteins F and HN with a panel of synthetic antibodies. J Virol. 2014 Oct; 88(20):11713-25. View in: PubMed

  60. Visualization of arrestin recruitment by a G-protein-coupled receptor. Nature. 2014 08 14; 512(7513):218-222. View in: PubMed

  61. Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. Cell Rep. 2014 Jul 10; 8(1):297-310. View in: PubMed

  62. Cell biology. New tricks for an old dimer. Science. 2014 May 16; 344(6185):703-4. View in: PubMed

  63. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nat Struct Mol Biol. 2014 Mar; 21(3):244-52. View in: PubMed

  64. Structure of active ?-arrestin-1 bound to a G-protein-coupled receptor phosphopeptide. Nature. 2013 May 02; 497(7447):137-41. View in: PubMed

  65. Generating conformation-specific synthetic antibodies to trap proteins in selected functional states. Methods. 2013 Mar 15; 60(1):3-14. View in: PubMed

  66. Substance P derivatives as versatile tools for specific delivery of various types of biomolecular cargo. Bioconjug Chem. 2012 Jan 18; 23(1):42-6. View in: PubMed

  67. Mechanism of activation gating in the full-length KcsA K+ channel. Proc Natl Acad Sci U S A. 2011 Jul 19; 108(29):11896-9. View in: PubMed

  68. Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins. Nat Struct Mol Biol. 2011 Apr; 18(4):437-42. View in: PubMed

  69. A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nat Struct Mol Biol. 2011 Jan; 18(1):100-6. View in: PubMed

  70. Characterization of engineered actin binding proteins that control filament assembly and structure. PLoS One. 2010 Nov 12; 5(11):e13960. View in: PubMed

  71. Keeping signaling in check. Structure. 2010 Mar 10; 18(3):275-6. View in: PubMed

  72. Role of a salt bridge in the model protein crambin explored by chemical protein synthesis: X-ray structure of a unique protein analogue, [V15A]crambin-alpha-carboxamide. Mol Biosyst. 2009 Jul; 5(7):750-6. View in: PubMed

  73. An engineered substance P variant for receptor-mediated delivery of synthetic antibodies into tumor cells. Proc Natl Acad Sci U S A. 2009 Jul 07; 106(27):11011-5. View in: PubMed

  74. Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods. Protein Sci. 2009 Jun; 18(6):1146-54. View in: PubMed

  75. Crystal structure of full-length KcsA in its closed conformation. Proc Natl Acad Sci U S A. 2009 Apr 21; 106(16):6644-9. View in: PubMed

  76. Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions. Proc Natl Acad Sci U S A. 2009 Feb 24; 106(8):2559-64. View in: PubMed

  77. X-ray structure of native scorpion toxin BmBKTx1 by racemic protein crystallography using direct methods. J Am Chem Soc. 2009 Feb 04; 131(4):1362-3. View in: PubMed

  78. Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces. Curr Opin Struct Biol. 2008 Aug; 18(4):499-506. View in: PubMed

  79. X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers. J Am Chem Soc. 2008 Jul 30; 130(30):9695-701. View in: PubMed

  80. Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold. Protein Sci. 2008 Jul; 17(7):1175-87. View in: PubMed

  81. The 1.38 A crystal structure of DmsD protein from Salmonella typhimurium, a proofreading chaperone on the Tat pathway. Proteins. 2008 May 01; 71(2):525-33. View in: PubMed

  82. Synthetic antibodies for specific recognition and crystallization of structured RNA. Proc Natl Acad Sci U S A. 2008 Jan 08; 105(1):82-7. View in: PubMed

  83. Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope. J Mol Biol. 2007 Nov 02; 373(4):941-53. View in: PubMed

  84. High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J Mol Biol. 2007 Nov 02; 373(4):924-40. View in: PubMed

  85. Exploring and designing protein function with restricted diversity. Curr Opin Chem Biol. 2007 Jun; 11(3):347-54. View in: PubMed

  86. Time-controlled microfluidic seeding in nL-volume droplets to separate nucleation and growth stages of protein crystallization. Angew Chem Int Ed Engl. 2006 Dec 11; 45(48):8156-60. View in: PubMed

  87. The role of protein dynamics in increasing binding affinity for an engineered protein-protein interaction established by H/D exchange mass spectrometry. Biochemistry. 2006 Jul 18; 45(28):8488-98. View in: PubMed

  88. Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning. J Biol Chem. 2006 Aug 04; 281(31):22378-22385. View in: PubMed

  89. Structure of bistramide A-actin complex at a 1.35 angstroms resolution. J Am Chem Soc. 2006 Mar 29; 128(12):3882-3. View in: PubMed

  90. Crystal structure and site 1 binding energetics of human placental lactogen. J Mol Biol. 2006 May 05; 358(3):773-84. View in: PubMed

  91. Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis. Nat Chem Biol. 2006 Mar; 2(3):139-43. View in: PubMed

  92. The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold. Proteins. 2006 Jan 01; 62(1):8-16. View in: PubMed

  93. Alternative views of functional protein binding epitopes obtained by combinatorial shotgun scanning mutagenesis. Protein Sci. 2005 Sep; 14(9):2405-13. View in: PubMed

  94. Shotgun alanine scanning shows that growth hormone can bind productively to its receptor through a drastically minimized interface. J Biol Chem. 2005 Jul 08; 280(27):25524-32. View in: PubMed

  95. Total chemical synthesis and X-ray crystal structure of a protein diastereomer: [D-Gln 35]ubiquitin. Angew Chem Int Ed Engl. 2005 Jun 20; 44(25):3852-6. View in: PubMed

  96. Intramolecular cooperativity in a protein binding site assessed by combinatorial shotgun scanning mutagenesis. J Mol Biol. 2005 Apr 01; 347(3):489-94. View in: PubMed

  97. The crystal structure of a quercetin 2,3-dioxygenase from Bacillus subtilis suggests modulation of enzyme activity by a change in the metal ion at the active site(s). Biochemistry. 2005 Jan 11; 44(1):193-201. View in: PubMed

  98. The high- and low-affinity receptor binding sites of growth hormone are allosterically coupled. Proc Natl Acad Sci U S A. 2004 Dec 07; 101(49):17078-83. View in: PubMed

  99. The structural basis for biological signaling, regulation, and specificity in the growth hormone-prolactin system of hormones and receptors. Adv Protein Chem. 2004; 68:147-69. View in: PubMed

  100. Dissecting the binding energy epitope of a high-affinity variant of human growth hormone: cooperative and additive effects from combining mutations from independently selected phage display mutagenesis libraries. Biochemistry. 2004 May 25; 43(20):6076-84. View in: PubMed

  101. The functional binding epitope of a high affinity variant of human growth hormone mapped by shotgun alanine-scanning mutagenesis: insights into the mechanisms responsible for improved affinity. J Mol Biol. 2003 Sep 05; 332(1):195-204. View in: PubMed

  102. Site2 binding energetics of the regulatory step of growth hormone-induced receptor homodimerization. Protein Sci. 2003 Sep; 12(9):1960-70. View in: PubMed

  103. The first semi-synthetic serine protease made by native chemical ligation. Protein Expr Purif. 2003 Jun; 29(2):185-92. View in: PubMed

  104. Determination of the energetics governing the regulatory step in growth hormone-induced receptor homodimerization. Proc Natl Acad Sci U S A. 2003 Feb 04; 100(3):952-7. View in: PubMed

  105. Functional promiscuity of squirrel monkey growth hormone receptor toward both primate and nonprimate growth hormones. Mol Biol Evol. 2002 Jul; 19(7):1083-92. View in: PubMed

  106. Structure of a phage display-derived variant of human growth hormone complexed to two copies of the extracellular domain of its receptor: evidence for strong structural coupling between receptor binding sites. J Mol Biol. 2002 Feb 15; 316(2):277-89. View in: PubMed

  107. High affinity RNase S-peptide variants obtained by phage display have a novel "hot-spot" of binding energy. Biochemistry. 2001 Nov 13; 40(45):13491-500. View in: PubMed

  108. The structure and activity of a monomeric interferon-gamma:alpha-chain receptor signaling complex. Structure. 2001 Feb 07; 9(2):155-63. View in: PubMed

  109. Ternary complex between placental lactogen and the extracellular domain of the prolactin receptor. Nat Struct Biol. 2000 Sep; 7(9):808-15. View in: PubMed

  110. Biosynthetic phage display: a novel protein engineering tool combining chemical and genetic diversity. Chem Biol. 2000 Apr; 7(4):263-74. View in: PubMed

  111. Deciphering the role of the electrostatic interactions involving Gly70 in eglin C by total chemical protein synthesis. Biochemistry. 2000 Apr 04; 39(13):3575-84. View in: PubMed

  112. The 2.0 A structure of bovine interferon-gamma; assessment of the structural differences between species. Acta Crystallogr D Biol Crystallogr. 2000 Jan; 56(Pt 1):14-24. View in: PubMed

  113. Probing intermolecular backbone H-bonding in serine proteinase-protein inhibitor complexes. Chem Biol. 1999 Jul; 6(7):419-27. View in: PubMed

  114. Crystallization of ovine placental lactogen in a 1:2 complex with the extracellular domain of the rat prolactin receptor. Acta Crystallogr D Biol Crystallogr. 1998 Nov 01; 54(Pt 6 Pt 2):1408-11. View in: PubMed

  115. Structural basis for cytokine hormone-receptor recognition and receptor activation. Adv Protein Chem. 1998; 52:67-108. View in: PubMed

  116. Crystallization and preliminary X-ray analysis of a 1:1 complex between a designed monomeric interferon-gamma and its soluble receptor. Protein Sci. 1998 Apr; 7(4):1057-60. View in: PubMed

  117. Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities. Protein Sci. 1997 Sep; 6(9):1806-24. View in: PubMed

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  122. The X-ray structure of a growth hormone-prolactin receptor complex. Nature. 1994 Dec 01; 372(6505):478-81. View in: PubMed

  123. Comparison of the intermediate complexes of human growth hormone bound to the human growth hormone and prolactin receptors. Protein Sci. 1994 Oct; 3(10):1697-705. View in: PubMed

  124. The production and X-ray structure determination of perdeuterated Staphylococcal nuclease. Biophys Chem. 1994 Dec; 53(1-2):15-25. View in: PubMed

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