Shohei Koide

The Recombinant Antibody Network

Affiliated withThe Recombinant Antibody Network The University of Chicago

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 33	2015

Other Publications

Article	Year
Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 11818562	2002
Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange. Journal of molecular biology\| PubMed ID: 12381326	2002
Calorimetric dissection of thermal unfolding of OspA, a predominantly beta-sheet protein containing a single-layer beta-sheet. Journal of molecular biology\| PubMed ID: 12419262	2002
Backbone dynamics and thermodynamics of Borrelia outer surface protein A. Journal of molecular biology\| PubMed ID: 12470954	2002
Engineered fibronectin type III domain with a RGDWXE sequence binds with enhanced affinity and specificity to human alphavbeta3 integrin. Journal of molecular biology\| PubMed ID: 12595259	2003
Exploring the potential of the monobody scaffold: effects of loop elongation on the stability of a fibronectin type III domain. Protein engineering\| PubMed ID: 12601141	2002
Mutation of Leu-536 in human estrogen receptor-alpha alters the coupling between ligand binding, transcription activation, and receptor conformation. The Journal of biological chemistry\| PubMed ID: 12736255	2003
Unfolding mechanics of multiple OspA substructures investigated with single molecule force spectroscopy. Journal of molecular biology\| PubMed ID: 14583195	2003
Conformational heterogeneity of an equilibrium folding intermediate quantified and mapped by scanning mutagenesis. Journal of molecular biology\| PubMed ID: 15099747	2004
Molecular recognition properties of FN3 monobodies that bind the Src SH3 domain. Chemistry & biology\| PubMed ID: 15217616	2004
Substrates for cell adhesion prepared via active site-directed immobilization of a protein domain. Langmuir : the ACS journal of surfaces and colloids\| PubMed ID: 15803670	2004
Structure-based design of a second-generation Lyme disease vaccine based on a C-terminal fragment of Borrelia burgdorferi OspA. Journal of molecular biology\| PubMed ID: 15935380	2005
Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry\| PubMed ID: 16008354	2005
High-affinity fragment complementation of a fibronectin type III domain and its application to stability enhancement. Protein science : a publication of the Protein Society\| PubMed ID: 16199661	2005
Conformation-specific affinity purification of proteins using engineered binding proteins: application to the estrogen receptor. Protein expression and purification\| PubMed ID: 16325424	2006
Understanding the human estrogen receptor-alpha using targeted mutagenesis. Molecular and cellular endocrinology\| PubMed ID: 16442702	2006
NMR assignment of rat Raf kinase inhibitor protein. Journal of biomolecular NMR\| PubMed ID: 16456706	2006
Atomic-resolution crystal structure of Borrelia burgdorferi outer surface protein A via surface engineering. Protein science : a publication of the Protein Society\| PubMed ID: 16823038	2006
Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 17041261	2007
Atomic structures of peptide self-assembly mimics. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17093048	2006
Identification of regions within the F domain of the human estrogen receptor alpha that are important for modulating transactivation and protein-protein interactions. Molecular endocrinology (Baltimore, Md.)\| PubMed ID: 17185393	2007
Hydrophobic surface burial is the major stability determinant of a flat, single-layer beta-sheet. Journal of molecular biology\| PubMed ID: 17335845	2007
High-affinity single-domain binding proteins with a binary-code interface. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17420456	2007
High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. Journal of molecular biology\| PubMed ID: 17825836	2007
Phage display for engineering and analyzing protein interaction interfaces. Current opinion in structural biology\| PubMed ID: 17870470	2007
Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope. Journal of molecular biology\| PubMed ID: 17888451	2007
pH dependence of stability of the 10th human fibronectin type III domain: a computational study. Biotechnology progress\| PubMed ID: 17935345	2008
Beta-strand flipping and slipping triggered by turn replacement reveal the opportunistic nature of beta-strand pairing. Journal of the American Chemical Society\| PubMed ID: 17985889	2007
Synthetic antibodies for specific recognition and crystallization of structured RNA. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18162543	2008
High-resolution structure of a self-assembly-competent form of a hydrophobic peptide captured in a soluble beta-sheet scaffold. Journal of molecular biology\| PubMed ID: 18367205	2008
Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold. Protein science : a publication of the Protein Society\| PubMed ID: 18445622	2008
Design of protein function leaps by directed domain interface evolution. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18445649	2008
A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces. Journal of molecular biology\| PubMed ID: 18602117	2008
Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces. Current opinion in structural biology\| PubMed ID: 18638552	2008
High-throughput analysis of the protein sequence-stability landscape using a quantitative yeast surface two-hybrid system and fragment reconstitution. Journal of molecular biology\| PubMed ID: 18674545	2008
Aromatic cross-strand ladders control the structure and stability of beta-rich peptide self-assembly mimics. Journal of molecular biology\| PubMed ID: 18762191	2008
The promiscuity of beta-strand pairing allows for rational design of beta-sheet face inversion. Journal of the American Chemical Society\| PubMed ID: 18842042	2008
Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies. Journal of molecular biology\| PubMed ID: 19038267	2009
Raf kinase inhibitory protein function is regulated via a flexible pocket and novel phosphorylation-dependent mechanism. Molecular and cellular biology\| PubMed ID: 19103740	2009
The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins. ACS chemical biology\| PubMed ID: 19298050	2009
Crystal structure of full-length KcsA in its closed conformation. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 19346472	2009
Engineering of recombinant crystallization chaperones. Current opinion in structural biology\| PubMed ID: 19477632	2009
Raf Kinase Inhibitory Protein protects cells against locostatin-mediated inhibition of migration. PloS one\| PubMed ID: 19551145	2009
Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution. Journal of molecular biology\| PubMed ID: 19646997	2009
Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules. Current opinion in biotechnology\| PubMed ID: 19700302	2009
Accelerating phage-display library selection by reversible and site-specific biotinylation. Protein engineering, design & selection : PEDS\| PubMed ID: 19737805	2009
Binding modes of thioflavin-T to the single-layer beta-sheet of the peptide self-assembly mimics. Journal of molecular biology\| PubMed ID: 19799914	2009
A peptide tag system for facile purification and single-molecule immobilization. Biochemistry\| PubMed ID: 19928925	2009
A designer ligand specific for Kv1.3 channels from a scorpion neurotoxin-based library. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20007782	2009
Minimalist design of water-soluble cross-beta architecture. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20133689	2010
Rational conversion of affinity reagents into label-free sensors for Peptide motifs by designed allostery. ACS chemical biology\| PubMed ID: 20143785	2010
A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain. Nature structural & molecular biology\| PubMed ID: 20357770	2010
Molecular mechanism of Thioflavin-T binding to amyloid fibrils. Biochimica et biophysica acta\| PubMed ID: 20399286	2010
Characterization of the Raf kinase inhibitory protein (RKIP) binding pocket: NMR-based screening identifies small-molecule ligands. PloS one\| PubMed ID: 20463977	2010
A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nature structural & molecular biology\| PubMed ID: 21151117	2011
Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 21518904	2011
Mechanism of activation gating in the full-length KcsA K+ channel. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 21730186	2011
Targeting the SH2-kinase interface in Bcr-Abl inhibits leukemogenesis. Cell\| PubMed ID: 22000011	2011
Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold. Journal of molecular biology\| PubMed ID: 22198408	2012
Target-binding proteins based on the 10th human fibronectin type III domain (¹⁰Fn3). Methods in enzymology\| PubMed ID: 22230568	2012
A delicate interplay of structure, dynamics, and thermodynamics for function: a high pressure NMR study of outer surface protein A. Biophysical journal\| PubMed ID: 22385863	2012
Identification of a tetratricopeptide repeat-like domain in the nicastrin subunit of γ-secretase using synthetic antibodies. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 22586122	2012
Structural insights for engineering binding proteins based on non-antibody scaffolds. Current opinion in structural biology\| PubMed ID: 22749196	2012
Affinity maturation of single-domain antibodies by yeast surface display. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 22886267	2012
T cell receptor-like recognition of tumor in vivo by synthetic antibody fragment. PloS one\| PubMed ID: 22916301	2012
Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay. Journal of molecular biology\| PubMed ID: 23041298	2012
CDR-H3 diversity is not required for antigen recognition by synthetic antibodies. Journal of molecular biology\| PubMed ID: 23219464	2013
Generating conformation-specific synthetic antibodies to trap proteins in selected functional states. Methods (San Diego, Calif.)\| PubMed ID: 23280336	2013
Structures of a Na+-coupled, substrate-bound MATE multidrug transporter. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23341609	2013
Generation of high-performance binding proteins for peptide motifs by affinity clamping. Methods in enzymology\| PubMed ID: 23422435	2013
Structure of active β-arrestin-1 bound to a G-protein-coupled receptor phosphopeptide. Nature\| PubMed ID: 23604254	2013
Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23922390	2013
Recombinant antibodies to histone post-translational modifications. Nature methods\| PubMed ID: 23955773	2013
Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23980151	2013
Directed network wiring identifies a key protein interaction in embryonic stem cell differentiation. Molecular cell\| PubMed ID: 24910098	2014
Visualization of arrestin recruitment by a G-protein-coupled receptor. Nature\| PubMed ID: 25043026	2014
Editorial overview: Engineering and design: raising the bar through innovation and integration. Current opinion in structural biology\| PubMed ID: 25175941	2014
Epigenetic dysregulation by nickel through repressive chromatin domain disruption. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 25246589	2014
Proof of dual-topology architecture of Fluc F- channels with monobody blockers. Nature communications\| PubMed ID: 25290819	2014
A Synthetic Antibody Fragment Targeting Nicastrin Affects Assembly and Trafficking of γ-Secretase. The Journal of biological chemistry\| PubMed ID: 25352592	2014