Shohei Koide

Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor.

Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange.

Calorimetric dissection of thermal unfolding of OspA, a predominantly beta-sheet protein containing a single-layer beta-sheet.

Backbone dynamics and thermodynamics of Borrelia outer surface protein A.

Engineered fibronectin type III domain with a RGDWXE sequence binds with enhanced affinity and specificity to human alphavbeta3 integrin.

Exploring the potential of the monobody scaffold: effects of loop elongation on the stability of a fibronectin type III domain.

Mutation of Leu-536 in human estrogen receptor-alpha alters the coupling between ligand binding, transcription activation, and receptor conformation.

Unfolding mechanics of multiple OspA substructures investigated with single molecule force spectroscopy.

Conformational heterogeneity of an equilibrium folding intermediate quantified and mapped by scanning mutagenesis.

Molecular recognition properties of FN3 monobodies that bind the Src SH3 domain.

Substrates for cell adhesion prepared via active site-directed immobilization of a protein domain.

Structure-based design of a second-generation Lyme disease vaccine based on a C-terminal fragment of Borrelia burgdorferi OspA.

Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library.

High-affinity fragment complementation of a fibronectin type III domain and its application to stability enhancement.

Conformation-specific affinity purification of proteins using engineered binding proteins: application to the estrogen receptor.

Understanding the human estrogen receptor-alpha using targeted mutagenesis.

NMR assignment of rat Raf kinase inhibitor protein.

Atomic-resolution crystal structure of Borrelia burgdorferi outer surface protein A via surface engineering.

Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain.

Atomic structures of peptide self-assembly mimics.

Identification of regions within the F domain of the human estrogen receptor alpha that are important for modulating transactivation and protein-protein interactions.

Hydrophobic surface burial is the major stability determinant of a flat, single-layer beta-sheet.

High-affinity single-domain binding proteins with a binary-code interface.

High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries.

Phage display for engineering and analyzing protein interaction interfaces.

Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope.

pH dependence of stability of the 10th human fibronectin type III domain: a computational study.

Beta-strand flipping and slipping triggered by turn replacement reveal the opportunistic nature of beta-strand pairing.

Synthetic antibodies for specific recognition and crystallization of structured RNA.

High-resolution structure of a self-assembly-competent form of a hydrophobic peptide captured in a soluble beta-sheet scaffold.

Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold.

Design of protein function leaps by directed domain interface evolution.

A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces.

Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces.

High-throughput analysis of the protein sequence-stability landscape using a quantitative yeast surface two-hybrid system and fragment reconstitution.

Aromatic cross-strand ladders control the structure and stability of beta-rich peptide self-assembly mimics.

The promiscuity of beta-strand pairing allows for rational design of beta-sheet face inversion.

Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies.

Raf kinase inhibitory protein function is regulated via a flexible pocket and novel phosphorylation-dependent mechanism.

The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins.

Crystal structure of full-length KcsA in its closed conformation.

Engineering of recombinant crystallization chaperones.

Raf Kinase Inhibitory Protein protects cells against locostatin-mediated inhibition of migration.

Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution.

Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules.

Accelerating phage-display library selection by reversible and site-specific biotinylation.

Binding modes of thioflavin-T to the single-layer beta-sheet of the peptide self-assembly mimics.

A peptide tag system for facile purification and single-molecule immobilization.

A designer ligand specific for Kv1.3 channels from a scorpion neurotoxin-based library.

Minimalist design of water-soluble cross-beta architecture.

Rational conversion of affinity reagents into label-free sensors for Peptide motifs by designed allostery.

A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain.

Molecular mechanism of Thioflavin-T binding to amyloid fibrils.

Characterization of the Raf kinase inhibitory protein (RKIP) binding pocket: NMR-based screening identifies small-molecule ligands.

A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination.

Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design.

Mechanism of activation gating in the full-length KcsA K+ channel.

Targeting the SH2-kinase interface in Bcr-Abl inhibits leukemogenesis.

Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold.

Target-binding proteins based on the 10th human fibronectin type III domain (¹⁰Fn3).

A delicate interplay of structure, dynamics, and thermodynamics for function: a high pressure NMR study of outer surface protein A.

Identification of a tetratricopeptide repeat-like domain in the nicastrin subunit of γ-secretase using synthetic antibodies.

Structural insights for engineering binding proteins based on non-antibody scaffolds.

Affinity maturation of single-domain antibodies by yeast surface display.

T cell receptor-like recognition of tumor in vivo by synthetic antibody fragment.

Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay.

CDR-H3 diversity is not required for antigen recognition by synthetic antibodies.

Generating conformation-specific synthetic antibodies to trap proteins in selected functional states.

Structures of a Na+-coupled, substrate-bound MATE multidrug transporter.

Generation of high-performance binding proteins for peptide motifs by affinity clamping.

Structure of active β-arrestin-1 bound to a G-protein-coupled receptor phosphopeptide.

Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme.

Recombinant antibodies to histone post-translational modifications.

Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains.

Directed network wiring identifies a key protein interaction in embryonic stem cell differentiation.

Visualization of arrestin recruitment by a G-protein-coupled receptor.

Editorial overview: Engineering and design: raising the bar through innovation and integration.

Epigenetic dysregulation by nickel through repressive chromatin domain disruption.

Proof of dual-topology architecture of Fluc F- channels with monobody blockers.

A Synthetic Antibody Fragment Targeting Nicastrin Affects Assembly and Trafficking of γ-Secretase.