Shohei Koide

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. pmc A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain
    John Wojcik
    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
    Nat Struct Mol Biol 17:519-27. 2010
  2. pmc T cell receptor-like recognition of tumor in vivo by synthetic antibody fragment
    Keith R Miller
    Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
    PLoS ONE 7:e43746. 2012
  3. pmc Generation of high-performance binding proteins for peptide motifs by affinity clamping
    Shohei Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA
    Methods Enzymol 523:285-302. 2013
  4. pmc Structural insights for engineering binding proteins based on non-antibody scaffolds
    Ryan N Gilbreth
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    Curr Opin Struct Biol 22:413-20. 2012
  5. pmc The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins
    Shohei Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    ACS Chem Biol 4:325-34. 2009
  6. pmc Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules
    Shohei Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, United States
    Curr Opin Biotechnol 20:398-404. 2009
  7. pmc Engineering of recombinant crystallization chaperones
    Shohei Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    Curr Opin Struct Biol 19:449-57. 2009
  8. ncbi request reprint Structure-based design of a second-generation Lyme disease vaccine based on a C-terminal fragment of Borrelia burgdorferi OspA
    Shohei Koide
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
    J Mol Biol 350:290-9. 2005
  9. pmc Hydrophobic surface burial is the major stability determinant of a flat, single-layer beta-sheet
    Shude Yan
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    J Mol Biol 368:230-43. 2007
  10. pmc Atomic structures of peptide self-assembly mimics
    Koki Makabe
    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 103:17753-8. 2006

Collaborators

Detail Information

Publications67

  1. pmc A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain
    John Wojcik
    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
    Nat Struct Mol Biol 17:519-27. 2010
    ..This work provides a design guideline for highly specific and potent inhibitors of a protein interaction domain and shows their utility in mechanistic and cellular investigations...
  2. pmc T cell receptor-like recognition of tumor in vivo by synthetic antibody fragment
    Keith R Miller
    Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
    PLoS ONE 7:e43746. 2012
    ..These antibody fragments have great potential for diagnosis and targeted drug delivery in cancer...
  3. pmc Generation of high-performance binding proteins for peptide motifs by affinity clamping
    Shohei Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA
    Methods Enzymol 523:285-302. 2013
    ..Affinity Clamping represents a major advance in protein design that is broadly applicable to the recognition of peptide motifs...
  4. pmc Structural insights for engineering binding proteins based on non-antibody scaffolds
    Ryan N Gilbreth
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    Curr Opin Struct Biol 22:413-20. 2012
    ..Furthermore, the structural features of these synthetic proteins produced under tightly controlled, directed evolution deepen our understanding of the underlying principles governing molecular recognition...
  5. pmc The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins
    Shohei Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    ACS Chem Biol 4:325-34. 2009
    ..In the near future, it seems likely that synthetic binding proteins will supersede natural antibodies for most purposes, and moreover, synthetic proteins will enable many new applications beyond the scope of natural proteins...
  6. pmc Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules
    Shohei Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, United States
    Curr Opin Biotechnol 20:398-404. 2009
    ....
  7. pmc Engineering of recombinant crystallization chaperones
    Shohei Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    Curr Opin Struct Biol 19:449-57. 2009
    ....
  8. ncbi request reprint Structure-based design of a second-generation Lyme disease vaccine based on a C-terminal fragment of Borrelia burgdorferi OspA
    Shohei Koide
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
    J Mol Biol 350:290-9. 2005
    ..Our strategy should be useful for further refining OspA-based vaccines and developing recombinant vaccines for other diseases...
  9. pmc Hydrophobic surface burial is the major stability determinant of a flat, single-layer beta-sheet
    Shude Yan
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    J Mol Biol 368:230-43. 2007
    ..These findings further suggest the importance of hydrophobic interactions within a beta-sheet layer in peptide self-assembly...
  10. pmc Atomic structures of peptide self-assembly mimics
    Koki Makabe
    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 103:17753-8. 2006
    ..Modeling shows how this conformational diversity, when propagated over a large number of peptide units, can lead to a substantial degree of nanoscale polymorphism of self-assemblies...
  11. pmc High-resolution structure of a self-assembly-competent form of a hydrophobic peptide captured in a soluble beta-sheet scaffold
    Koki Makabe
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
    J Mol Biol 378:459-67. 2008
    ..The ability of the PSAM to "solubilize" an otherwise insoluble peptide stretch suggests the potential of the PSAM approach to the characterization of self-assembling peptides...
  12. pmc Beta-strand flipping and slipping triggered by turn replacement reveal the opportunistic nature of beta-strand pairing
    Koki Makabe
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
    J Am Chem Soc 129:14661-9. 2007
    ....
  13. pmc Characterization of the Raf kinase inhibitory protein (RKIP) binding pocket: NMR-based screening identifies small-molecule ligands
    Anne N Shemon
    Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 5:e10479. 2010
    ..In addition to phospholipids, other ligands have been reported to bind this domain; however their binding properties remain uncharacterized...
  14. pmc A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces
    Ryan N Gilbreth
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    J Mol Biol 381:407-18. 2008
    ....
  15. pmc Synthetic antibodies for specific recognition and crystallization of structured RNA
    Jing Dong Ye
    Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 105:82-7. 2008
    ..These findings yield valuable insights for engineering of Fabs as RNA-binding modules and facilitate further development of Fabs as possible therapeutic drugs and biochemical tools to explore RNA biology...
  16. pmc Atomic-resolution crystal structure of Borrelia burgdorferi outer surface protein A via surface engineering
    Koki Makabe
    Department of Biochemistry and Molecular Biology, The University of Chicago, Illinois 60637, USA
    Protein Sci 15:1907-14. 2006
    ..This work demonstrates the utility of extensive surface mutation in crystallizing recalcitrant proteins and dramatically improving the resolution of crystal structures, and provides new insights into the stabilization mechanism of OspA...
  17. pmc Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution
    Jin Huang
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    J Mol Biol 392:1221-31. 2009
    ..These attributes of directed domain-interface evolution provide facile means to generate synthetic proteins with a broad range of functions...
  18. pmc Design of protein function leaps by directed domain interface evolution
    Jin Huang
    Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 105:6578-83. 2008
    ..The prevalence and variety of natural interaction domains suggest that numerous new functions can be designed by using directed domain interface evolution...
  19. pmc Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design
    Ryan N Gilbreth
    Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 108:7751-6. 2011
    ..The monobodies inhibited SUMO1/SIM interactions and, unexpectedly, also inhibited SUMO1 conjugation. These high-affinity and isoform-specific inhibitors will enhance mechanistic and cellular investigations of SUMO biology...
  20. pmc Aromatic cross-strand ladders control the structure and stability of beta-rich peptide self-assembly mimics
    Matthew Biancalana
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    J Mol Biol 383:205-13. 2008
    ..Our results therefore provide a rationale for the abundance of aromatic amino acids in fibril-forming peptides and establish important roles of cross-strand Tyr ladders in the structure and stability of beta-rich peptide self-assemblies...
  21. doi request reprint Target-binding proteins based on the 10th human fibronectin type III domain (¹⁰Fn3)
    Shohei Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA
    Methods Enzymol 503:135-56. 2012
    ..In addition to performing well as specific in vitro detection reagents and research tools, (10)Fn3-based binding proteins are being developed as therapeutics, with the most advanced candidate currently in Phase II clinical trials...
  22. pmc Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope
    Akiko Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    J Mol Biol 373:941-53. 2007
    ..More generally, they suggest that highly functional interfaces can be designed without closely mimicking natural interfaces...
  23. pmc Crystal structure of full-length KcsA in its closed conformation
    Serdar Uysal
    Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 106:6644-9. 2009
    ..Functional analysis of the full-length KcsA-Fab complex suggests that the C-terminal bundle remains whole during gating. We suggest that this structure likely represents the physiologically relevant closed conformation of KcsA...
  24. pmc High-throughput analysis of the protein sequence-stability landscape using a quantitative yeast surface two-hybrid system and fragment reconstitution
    Sanjib Dutta
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    J Mol Biol 382:721-33. 2008
    ..Our method provides a powerful means for the rapid assessment of the stability of many variants, for the systematic assessment of the contribution of different factors to protein stability, and for enhancement of the protein stability...
  25. pmc Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold
    Valentina Tereshko
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
    Protein Sci 17:1175-87. 2008
    ..Together with the presence of high-throughput selection systems (e.g., phage display libraries) for V(H)H, the enhanced V(H)H domain described here will be an excellent scaffold for producing effective crystallization chaperones...
  26. pmc Identification of a tetratricopeptide repeat-like domain in the nicastrin subunit of γ-secretase using synthetic antibodies
    Xulun Zhang
    Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 109:8534-9. 2012
    ..Taken together, these studies offer provocative insights pertaining to the structural basis for nicastrin function as a "substrate receptor" within the γ-secretase complex...
  27. pmc High-affinity single-domain binding proteins with a binary-code interface
    Akiko Koide
    Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 104:6632-7. 2007
    ....
  28. pmc Accelerating phage-display library selection by reversible and site-specific biotinylation
    Akiko Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    Protein Eng Des Sel 22:685-90. 2009
    ..Together, these results establish a method with the potential to streamline and enhance many binding-protein engineering experiments...
  29. ncbi request reprint Conformational heterogeneity of an equilibrium folding intermediate quantified and mapped by scanning mutagenesis
    Shude Yan
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    J Mol Biol 338:811-25. 2004
    ..Our results are consistent with the presence of multiple minima in a rugged energy landscape predicted from theoretical studies. The method described here provides a promising means to probe a complex folding energy landscape...
  30. pmc Minimalist design of water-soluble cross-beta architecture
    Matthew Biancalana
    Department of Biochemistry and Molecular Biology, The University of Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 107:3469-74. 2010
    ..Our results provide a new route for accessing the cross-beta structure and expanding the scope of protein design...
  31. ncbi request reprint Exploring the potential of the monobody scaffold: effects of loop elongation on the stability of a fibronectin type III domain
    Vincent Batori
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Protein Eng 15:1015-20. 2002
    ..These results suggest that all loops, except for the EF loop, can be used for engineering a binding site, thus demonstrating excellent properties of the monobody scaffold...
  32. ncbi request reprint Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain
    Akiko Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, IL, USA
    Methods Mol Biol 352:95-109. 2007
    ..These desirable physical properties render the FNfn10 scaffold compatible with virtually any display technologies. This chapter describes methods for library construction and screening and for the production of monobodies...
  33. pmc Recombinant antibodies to histone post-translational modifications
    Takamitsu Hattori
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA
    Nat Methods 10:992-5. 2013
    ..These recombinant antibodies performed well in common epigenetics applications, and enabled us to identify positive and negative correlations among histone PTMs. ..
  34. pmc Generating conformation-specific synthetic antibodies to trap proteins in selected functional states
    Marcin Paduch
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    Methods 60:3-14. 2013
    ..The methods described are generalizable and can be adapted to other in vitro direct evolution approaches based on yeast or mRNA display...
  35. ncbi request reprint Engineered fibronectin type III domain with a RGDWXE sequence binds with enhanced affinity and specificity to human alphavbeta3 integrin
    Julie Richards
    Department of Microbiology and Immunology, University of Rochester Medical Center, 575 Elmwood Avenue, Box 672, Rochester, NY 14642, USA
    J Mol Biol 326:1475-88. 2003
    ..These properties, combined with the small, monomeric, cysteine-free and highly stable structure of FNfn10-3JCLI4, may make this protein useful in future applications involving detection and targeting of alphavbeta3-positive cells...
  36. pmc Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies
    Matthew Biancalana
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    J Mol Biol 385:1052-63. 2009
    ..Our work thus provides structural insights into how this widely used dye recognizes a prominent subset of peptide self-assemblies, and proposes a strategy to elucidate the mechanisms of fibril-ligand interactions...
  37. pmc A designer ligand specific for Kv1.3 channels from a scorpion neurotoxin-based library
    Zoltan Takacs
    Department of Pediatrics and Institute of Molecular Pediatric Sciences, Pritzker School of Medicine, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 106:22211-6. 2009
    ..This scaffold-based/target-biased strategy overcomes many obstacles to production of selective toxins...
  38. pmc Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains
    Fern Sha
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637 and Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Federale de Lausanne, CH 1015 Lausanne, Switzerland
    Proc Natl Acad Sci U S A 110:14924-9. 2013
    ..Our results delineate a hierarchy of function for the SH2 domains of SHP2 and validate monobodies as potent and specific antagonists of protein-protein interactions in cancer cells. ..
  39. ncbi request reprint Conformation-specific affinity purification of proteins using engineered binding proteins: application to the estrogen receptor
    Jin Huang
    Department of Biochemistry and Molecular Biology, The University of Chicago, IL 60637, USA
    Protein Expr Purif 47:348-54. 2006
    ..Our strategy should be generally applicable to the preparation of conformationally homogeneous protein samples...
  40. pmc Mechanism of activation gating in the full-length KcsA K+ channel
    Serdar Uysal
    Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 108:11896-9. 2011
    ..We suggest that by limiting the extent to which the inner gate can open, the cytoplasmic domain also modulates the level of inactivation occurring at the selectivity filter...
  41. doi request reprint The promiscuity of beta-strand pairing allows for rational design of beta-sheet face inversion
    Koki Makabe
    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
    J Am Chem Soc 130:14370-1. 2008
    ..This work suggests a simple but effective strategy for designing and controlling nanomaterials based on beta-rich peptide self-assemblies...
  42. pmc A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination
    Yelena Koldobskaya
    Department of Chemistry, University of Chicago, Chicago, Illinois, USA
    Nat Struct Mol Biol 18:100-6. 2011
    ....
  43. pmc Raf kinase inhibitory protein function is regulated via a flexible pocket and novel phosphorylation-dependent mechanism
    Alexey E Granovsky
    Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
    Mol Cell Biol 29:1306-20. 2009
    ..This mechanism is an example of an emerging theme involving the regulation of signaling proteins and their interaction with effectors at the level of protein dynamics...
  44. pmc Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme
    Lauren A McCord
    Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 110:13827-32. 2013
    ..Together, our data provide insights into the conformational changes of IDE that govern the selective destruction of amyloidogenic peptides...
  45. ncbi request reprint Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library
    Abhishek K Jha
    Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
    Biochemistry 44:9691-702. 2005
    ..In addition, these propensities are often strongly affected by both the chemical nature and the conformation of neighboring residues, contrary to the Flory isolated residue hypothesis...
  46. doi request reprint Affinity maturation of single-domain antibodies by yeast surface display
    Akiko Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
    Methods Mol Biol 911:431-43. 2012
    ..An example is included where we also exploit a complementary strength of phage display in generating larger sequence diversity prior to library sorting with yeast surface display...
  47. pmc Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold
    Akiko Koide
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
    J Mol Biol 415:393-405. 2012
    ..Together, this work illustrates the utilization of different surfaces of a single immunoglobulin-like scaffold to generate binding proteins with distinct characteristics...
  48. ncbi request reprint Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange
    Shude Yan
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY 14642, USA
    J Mol Biol 323:363-75. 2002
    ..This method, which we term EX2/EX1 HX, should be a powerful tool for characterizing the complex folding mechanisms exhibited by the majority of proteins...
  49. pmc A peptide tag system for facile purification and single-molecule immobilization
    Jin Huang
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
    Biochemistry 48:11834-6. 2009
    ....
  50. pmc High-affinity fragment complementation of a fibronectin type III domain and its application to stability enhancement
    Sanjib Dutta
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    Protein Sci 14:2838-48. 2005
    ..One of the identified mutations significantly increased the stability of the uncut wild-type protein, proving that fragment complementation can be used as a novel strategy for the selection of proteins with enhanced stability...
  51. pmc Raf Kinase Inhibitory Protein protects cells against locostatin-mediated inhibition of migration
    Anne N Shemon
    Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
    PLoS ONE 4:e6028. 2009
    ..Since an organic compound, locostatin, was reported to bind RKIP and inhibit cell migration by a Raf-dependent mechanism, we addressed the role of RKIP in locostatin function...
  52. pmc Structures of a Na+-coupled, substrate-bound MATE multidrug transporter
    Min Lu
    Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
    Proc Natl Acad Sci U S A 110:2099-104. 2013
    ..Collectively, our findings provide an important step toward a detailed and mechanistic understanding of multidrug transport...
  53. pmc Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay
    Shingo Nishikori
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    J Mol Biol 424:391-9. 2012
    ..Furthermore, using this method, we identified additional factors potentially affecting the interpretation of ChIP experiments...
  54. pmc Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor
    Akiko Koide
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Proc Natl Acad Sci U S A 99:1253-8. 2002
    ....
  55. ncbi request reprint Identification of regions within the F domain of the human estrogen receptor alpha that are important for modulating transactivation and protein-protein interactions
    Akiko Koide
    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
    Mol Endocrinol 21:829-42. 2007
    ..These results show that regions within the F domain of the hERalpha selectively modulate its activity and its interactions with other proteins...
  56. ncbi request reprint Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces
    Anthony A Kossiakoff
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, United States
    Curr Opin Struct Biol 18:499-506. 2008
    ..Synthetic binding proteins are beginning to be used as a powerful crystallization tool to attack important structural biology problems that are recalcitrant to crystallization using traditional methods...
  57. ncbi request reprint NMR assignment of rat Raf kinase inhibitor protein
    Matthew C Clark
    Department of Neurobiology, Pharmacology and Physiology, Ben May Institute for Cancer Research, Chicago, Illinois 60637, USA
    J Biomol NMR 36:4. 2006
  58. ncbi request reprint Directed network wiring identifies a key protein interaction in embryonic stem cell differentiation
    Norihisa Yasui
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
    Mol Cell 54:1034-41. 2014
    ..We propose that this directed wiring approach will be of general utility in functionally annotating specific PPIs. ..
  59. pmc Rational conversion of affinity reagents into label-free sensors for Peptide motifs by designed allostery
    Jin Huang
    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637
    ACS Chem Biol 5:273-7. 2010
    ..Because diverse affinity clamps can be engineered, our strategy provides a general platform to generate a repertoire of genetically encoded, label-free sensors for peptide motifs...
  60. ncbi request reprint Unfolding mechanics of multiple OspA substructures investigated with single molecule force spectroscopy
    Rukman Hertadi
    Laboratory of Biodynamics, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta cho, Midori ku, Yokohama, Kanagawa 226 8501, Japan
    J Mol Biol 333:993-1002. 2003
    ..This work demonstrates that AFM study of monomeric proteins can elucidate details of the intramolecular mechanics of protein substructures...
  61. ncbi request reprint Backbone dynamics and thermodynamics of Borrelia outer surface protein A
    Norma H Pawley
    Department of Molecular Biology and Genetics, Cornell University, 239 Biotechnology Building, Ithaca, NY 14853, USA
    J Mol Biol 324:991-1002. 2002
    ..This increase in heat capacity may help to explain the unexpected thermal stability of the unusual single-layer beta-sheet...
  62. ncbi request reprint Calorimetric dissection of thermal unfolding of OspA, a predominantly beta-sheet protein containing a single-layer beta-sheet
    Tomoko Nakagawa
    Graduate School of Science and Technology, Kobe University, Nadaku, Kobe, Japan
    J Mol Biol 323:751-62. 2002
    ..These thermodynamic analyses demonstrated that it is possible to maintain protein tertiary structure by making effective use of an unusual amino acid composition...
  63. ncbi request reprint Substrates for cell adhesion prepared via active site-directed immobilization of a protein domain
    William L Murphy
    Langmuir 20:1026-30. 2004
  64. ncbi request reprint Mutation of Leu-536 in human estrogen receptor-alpha alters the coupling between ligand binding, transcription activation, and receptor conformation
    Changqing Zhao
    Department of Physiology, Wayne State University School of Medicine, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, USA
    J Biol Chem 278:27278-86. 2003
    ..These results show that Leu-536 is critical in coupling the binding of ligand to the modulation of the conformation and activity of ERalpha...
  65. ncbi request reprint Molecular recognition properties of FN3 monobodies that bind the Src SH3 domain
    Ece Karatan
    Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
    Chem Biol 11:835-44. 2004
    ..The strongest binder was able to pull down full-length c-Src from murine fibroblast cell extracts, further demonstrating the potential of this scaffold for use as an antibody mimetic...
  66. ncbi request reprint Phage display for engineering and analyzing protein interaction interfaces
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Curr Opin Struct Biol 17:481-7. 2007
    ....
  67. ncbi request reprint Understanding the human estrogen receptor-alpha using targeted mutagenesis
    Debra F Skafar
    Department of Physiology, Wayne State University School of Medicine, 540 E Canfield, Detroit, MI 48201, USA
    Mol Cell Endocrinol 246:83-90. 2006
    ..Overall, these results show that combining structure-based hypotheses with functional tests of the ER's activity can identify regions and interactions that are important in the ligand-stimulated activity of the protein...

Research Grants14

  1. Rational generation of directed protein-capture reagents
    Shohei Koide; Fiscal Year: 2010
    ..This innovative and powerful technology will fill a major void in the currently available molecular tools and will have a major impact on virtually all areas of molecular biomedical sciences, diagnosis and drug development. ..
  2. Nuclear receptor probed with designer binding proteins
    Shohei Koide; Fiscal Year: 2005
    ..We expect that results from this project will fill a large gap that presently exists between out knowledge gained from the static ..
  3. STRUCTURE AND STABILITY OF SINGLE-LAYER BETA-SHEETS
    Shohei Koide; Fiscal Year: 2005
    ..Outcomes of this study will also provide important information for structural genomics and de novo protein design. ..
  4. Nuclear receptor probed with designer binding proteins
    Shohei Koide; Fiscal Year: 2004
    ..We expect that results from this project will fill a large gap that presently exists between out knowledge gained from the static ..
  5. STRUCTURE AND STABILITY OF SINGLE-LAYER BETA-SHEETS
    Shohei Koide; Fiscal Year: 2002
    ..Outcomes of this study will also provide important information for structural genomics and de novo protein design. ..
  6. STRUCTURE AND STABILITY OF SINGLE-LAYER BETA-SHEETS
    Shohei Koide; Fiscal Year: 2003
    ..Outcomes of this study will also provide important information for structural genomics and de novo protein design. ..
  7. Rational generation of directed protein-capture reagents
    Shohei Koide; Fiscal Year: 2009
    ..This innovative and powerful technology will fill a major void in the currently available molecular tools and will have a major impact on virtually all areas of molecular biomedical sciences, diagnosis and drug development. ..
  8. STRUCTURE AND STABILITY OF SINGLE-LAYER BETA-SHEETS
    Shohei Koide; Fiscal Year: 2000
    ..Outcomes of this study will also provide important information for structural genomics and de novo protein design. ..
  9. Nuclear receptor probed with designer binding proteins
    Shohei Koide; Fiscal Year: 2003
    ..We expect that results from this project will fill a large gap that presently exists between out knowledge gained from the static ..
  10. STRUCTURE AND STABILITY OF SINGLE-LAYER BETA-SHEETS
    Shohei Koide; Fiscal Year: 2002
    ..Outcomes of this study will also provide important information for structural genomics and de novo protein design. ..
  11. Nuclear receptor probed with designer binding proteins
    Shohei Koide; Fiscal Year: 2002
    ..We expect that results from this project will fill a large gap that presently exists between out knowledge gained from the static ..
  12. STRUCTURE AND STABILITY OF SINGLE-LAYER BETA-SHEETS
    Shohei Koide; Fiscal Year: 2001
    ..Outcomes of this study will also provide important information for structural genomics and de novo protein design. ..