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The Importance of Being Tyrosine: Lessons in Molecular Recognition from Minimalist Synthetic Binding Proteins

https://doi.org/10.1021/cb800314v
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Molecular interactions at the T cell–antigen-presenting cell interface
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Engineered proteins as specific binding reagents
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Tyrosine Plays a Dominant Functional Role in the Paratope of a Synthetic Antibody Derived from a Four Amino Acid Code
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The modular architecture of protein–protein binding interfaces
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Molecular basis for the preferential cleft recognition by dromedary heavy-chain antibodies
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High-affinity single-domain binding proteins with a binary-code interface
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Synthetic antibodies for specific recognition and crystallization of structured RNA
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In vitro evolution of a T cell receptor with high affinity for peptide/MHC
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Crystal structure of full-length KcsA in its closed conformation
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Two-state selection of conformation-specific antibodies
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Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity
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Hydroxyarginine-containing Polyphenolic Proteins in the Adhesive Plaques of the Marine Mussel Mytilus edulis
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Receptor-selective Variants of Human Vascular Endothelial Growth Factor
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Shotgun Alanine Scanning Shows That Growth Hormone Can Bind Productivelyto Its Receptor through a Drastically MinimizedInterface
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Isolation of Intracellular Proteinase Inhibitors Derived from Designed Ankyrin Repeat Proteins by Genetic Screening
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Polyphenolic Substance of Mytilus edulis : Novel Adhesive Containing L-Dopa and Hydroxyproline
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A Hot Spot of Binding Energy in a Hormone-Receptor Interface

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inferred← citeshttps://doi.org/10.1021/acschembio.5b00440openalex-snapshot
Tyrosine-Specific Chemical Modification with in Situ Hemin-Activated Luminol Derivatives
inferred← citeshttps://doi.org/10.1021/acscombsci.8b00182openalex-snapshot
Biophysical Characterization Platform Informs Protein Scaffold Evolvability
inferred← citeshttps://doi.org/10.1021/acsmaterialsau.5c00049openalex-snapshot
An Orthogonal Supramolecular Approach toward Protein Binding and Protein Sensing Using Dendrimers as Scaffolds for the Noncovalent Assembly of Binding and Sensing Groups
inferred← citeshttps://doi.org/10.1021/acsomega.3c06996openalex-snapshot
Predictive Models and Impact of Interfacial Contacts and Amino Acids on Protein–Protein Binding Affinity
inferred← citeshttps://doi.org/10.1021/acssynbio.3c00409openalex-snapshot
Hyperstable Synthetic Mini-Proteins as Effective Ligand Scaffolds
inferred← citeshttps://doi.org/10.1021/ar300234copenalex-snapshot
Protein Tyrosine Nitration: Biochemical Mechanisms and Structural Basis of Functional Effects
inferred← citeshttps://doi.org/10.1021/bc1003982openalex-snapshot
Site-Specific Protein Cross-Linking by Peroxidase-Catalyzed Activation of a Tyrosine-Containing Peptide Tag
inferred← citeshttps://doi.org/10.1021/bc500137jopenalex-snapshot
Thiocarbamate-Linked Polysulfonate–Peptide Conjugates As Selective Hepatocyte Growth Factor Receptor Binders
inferred← citeshttps://doi.org/10.1021/bi1006223openalex-snapshot
Structure−Activity Relationship Analysis of Peptides Targeting the EphA2 Receptor
inferred← citeshttps://doi.org/10.1021/bi3002924openalex-snapshot
A Propensity Scale for Type II Polyproline Helices (PPII): Aromatic Amino Acids in Proline-Rich Sequences Strongly Disfavor PPII Due to Proline–Aromatic Interactions
inferred← citeshttps://doi.org/10.1021/bi500696kopenalex-snapshot
Tunable Control of Polyproline Helix (PPII) Structure via Aromatic Electronic Effects: An Electronic Switch of Polyproline Helix
inferred← citeshttps://doi.org/10.1021/bm2007168openalex-snapshot
Larger Helical Populations in Peptides Derived from the Dimerization Helix of the Capsid Protein of HIV-1 Results in Peptide Binding toward Regions Other than the “Hotspot” Interface
inferred← citeshttps://doi.org/10.1021/cb2000346openalex-snapshot
Small Molecule Inhibition of the TNF Family Cytokine CD40 Ligand through a Subunit Fracture Mechanism
inferred← citeshttps://doi.org/10.1021/cb400675dopenalex-snapshot
Structure Determinants for the Substrate Specificity of Acyl-CoA Δ9 Desaturases from a Marine Copepod
inferred← citeshttps://doi.org/10.1021/cn500014uopenalex-snapshot
Transthyretin-Derived Peptides as β-Amyloid Inhibitors
inferred← citeshttps://doi.org/10.1021/jacs.4c04035openalex-snapshot
Site-Specific Antibody Prodrugs via S -Arylation: a Bioconjugation Approach Toward Masked Tyrosine Analogues
inferred← citeshttps://doi.org/10.1021/jacs.5c13307openalex-snapshot
Baited SELEX: Drug-Directed Selection of Aptamers to PSMA for In Vivo Targeting of Prostate Cancer Xenografts in Mice
inferred← citeshttps://doi.org/10.1021/jp4106037openalex-snapshot
Oxidation and Nitration of Tyrosine by Ozone and Nitrogen Dioxide: Reaction Mechanisms and Biological and Atmospheric Implications
inferred← citeshttps://doi.org/10.1021/ol202947fopenalex-snapshot
Synthesis of Thiophenylalanine-containing Peptides via Cu(I)-mediated Cross-Coupling
inferred← citeshttps://doi.org/10.1021/pr401117mopenalex-snapshot
Identification of Nitrated Immunoglobulin Variable Regions in the HIV-Infected Human Brain: Implications in HIV Infection and Immune Response
inferred← citeshttps://doi.org/10.1038/nature12463openalex-snapshot
A recipe for ligand-binding proteins
inferred← citeshttps://doi.org/10.1038/s41467-021-27184-wopenalex-snapshot
Design of a methotrexate-controlled chemical dimerization system and its use in bio-electronic devices
inferred← citeshttps://doi.org/10.1038/s41467-023-44083-4openalex-snapshot
Characterizations of a neutralizing antibody broadly reactive to multiple gluten peptide:HLA-DQ2.5 complexes in the context of celiac disease
inferred← citeshttps://doi.org/10.1038/s41586-022-05259-yopenalex-snapshot
The γδ IEL effector API5 masks genetic susceptibility to Paneth cell death
inferred← citeshttps://doi.org/10.1038/s41589-019-0229-2openalex-snapshot
Side chain determinants of biopolymer function during selection and replication
inferred← citeshttps://doi.org/10.1038/s41598-020-80354-6openalex-snapshot
Selection and characterisation of Affimers specific for CEA recognition
inferred← citeshttps://doi.org/10.1038/s41598-021-93626-6openalex-snapshot
Important innate differences in determining symbiotic responsiveness in host and non-hosts of arbuscular mycorrhiza
inferred← citeshttps://doi.org/10.1038/s44318-024-00200-7openalex-snapshot
The fitness cost of spurious phosphorylation
inferred← citeshttps://doi.org/10.1039/b927393jopenalex-snapshot
The functional capacity of the natural amino acids for molecular recognition
inferred← citeshttps://doi.org/10.1039/c2ay25389eopenalex-snapshot
Homogeneous electrogenerated chemiluminescence peptide-based method for determination of troponin I
inferred← citeshttps://doi.org/10.1039/c2mb25178gopenalex-snapshot
A cardiac tissue-specific binding agent of troponin I
inferred← citeshttps://doi.org/10.1039/c4mb00018hopenalex-snapshot
Understanding and applying tyrosine biochemical diversity
inferred← citeshttps://doi.org/10.1039/c5ra00192gopenalex-snapshot
Environmentally responsive amino acid-bioconjugated dynamic covalent copolymer as a versatile scaffold for conjugation
inferred← citeshttps://doi.org/10.1039/c7me00091jopenalex-snapshot
Identifying peptide sequences that can control the assembly of gold nanostructures
inferred← citeshttps://doi.org/10.1039/c9ob01471copenalex-snapshot
Modifications of amino acids using arenediazonium salts
inferred← citeshttps://doi.org/10.1039/d3nr03499bopenalex-snapshot
Photoinduced force microscopy as a novel method for the study of microbial nanostructures
inferred← citeshttps://doi.org/10.1039/d4md00073kopenalex-snapshot
The importance of tyrosines in multimers of cyclic RGD nonapeptides: towards αvβ6-integrin targeted radiotherapeutics
inferred← citeshttps://doi.org/10.1039/d5ma00736dopenalex-snapshot
A light responsive single amino acid-based supramolecular hydrogel for photo-controlled vitamin release
inferred← citeshttps://doi.org/10.1039/d5sc05199aopenalex-snapshot
Desulfurative modification of cysteine residues in peptides and proteins via the installation and photoexcitation of thieno[2,3- c ]-pyrroles
inferred← citeshttps://doi.org/10.1042/ebc20190052openalex-snapshot
3-Nitrotyrosine and related derivatives in proteins: precursors, radical intermediates and impact in function
inferred← citeshttps://doi.org/10.1073/pnas.1401131111openalex-snapshot
Origins of specificity and affinity in antibody–protein interactions
inferred← citeshttps://doi.org/10.1073/pnas.1511996112openalex-snapshot
Generation of MANAbodies specific to HLA-restricted epitopes encoded by somatically mutated genes
inferred← citeshttps://doi.org/10.1073/pnas.2100588118openalex-snapshot
Structures suggest an approach for converting weak self-peptide tumor antigens into superagonists for CD8 T cells in cancer
inferred← citeshttps://doi.org/10.1073/pnas.2317307121openalex-snapshot
A general approach for selection of epitope-directed binders to proteins
inferred← citeshttps://doi.org/10.1074/jbc.m117.814152openalex-snapshot
Subtle changes at the variable domain interface of the T-cell receptor can strongly increase affinity
inferred← citeshttps://doi.org/10.1074/jbc.ra119.010251openalex-snapshot
An engineered antibody fragment targeting mutant β-catenin via major histocompatibility complex I neoantigen presentation
inferred← citeshttps://doi.org/10.1080/02648725.2010.10648145openalex-snapshot
Phage display and molecular imaging: expanding fields of vision in living subjects
inferred← citeshttps://doi.org/10.1080/07391102.2023.2252077openalex-snapshot
Categorization of hotspots into three types – weak, moderate and strong to distinguish protein–protein versus protein–peptide interactions
inferred← citeshttps://doi.org/10.1080/19420862.2018.1550320openalex-snapshot
Effective binding to protein antigens by antibodies from antibody libraries designed with enhanced protein recognition propensities
inferred← citeshttps://doi.org/10.1080/19420862.2020.1803646openalex-snapshot
Affinity maturation of antibodies by combinatorial codon mutagenesis versus error-prone PCR
inferred← citeshttps://doi.org/10.1080/19420862.2023.2268255openalex-snapshot
A window into the human immune system: comprehensive characterization of the complexity of antibody complementary-determining regions in functional antibodies
inferred← citeshttps://doi.org/10.1080/19420862.2024.2362432openalex-snapshot
Structural analysis of light chain-driven bispecific antibodies targeting CD47 and PD-L1
inferred← citeshttps://doi.org/10.1080/19420889.2023.2203626openalex-snapshot
Computational and cellular exploration of the protein-protein interaction between Vibrio fischeri STAS domain protein SypA and serine kinase SypE
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad392openalex-snapshot
Understanding the complementarity and plasticity of antibody–antigen interfaces
inferred← citeshttps://doi.org/10.1093/bioinformatics/btt369openalex-snapshot
Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server
inferred← citeshttps://doi.org/10.1093/jb/mvaa147openalex-snapshot
A sweet protein monellin as a non-antibody scaffold for synthetic binding proteins
inferred← citeshttps://doi.org/10.1093/protein/gzaa016openalex-snapshot
Understanding microcystin-LR antibody binding interactions using in silico docking and in vitro mutagenesis
inferred← citeshttps://doi.org/10.1093/protein/gzaa028openalex-snapshot
Structure- and sequence-based design of synthetic single-domain antibody libraries
inferred← citeshttps://doi.org/10.1093/protein/gzp083openalex-snapshot
The full amino acid repertoire is superior to serine/tyrosine for selection of high affinity immunoglobulin G binders from the fibronectin scaffold
inferred← citeshttps://doi.org/10.1093/protein/gzq017openalex-snapshot
Identification and characterization of β-lactamase inhibitor protein-II (BLIP-II) interactions with β-lactamases using phage display
inferred← citeshttps://doi.org/10.1093/protein/gzv067openalex-snapshot
Overcoming a species-specificity barrier in development of an inhibitory antibody targeting a modulator of tumor stroma
inferred← citeshttps://doi.org/10.1093/protein/gzw050openalex-snapshot
A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces
inferred← citeshttps://doi.org/10.1093/protein/gzz007openalex-snapshot
Computational-guided determination of the functional role of 447-52D long CDRH3
inferred← citeshttps://doi.org/10.1097/qad.0000000000001108openalex-snapshot
Development of synthetic light-chain antibodies as novel and potent HIV fusion inhibitors
inferred← citeshttps://doi.org/10.1098/rstb.2011.0144openalex-snapshot
Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment
inferred← citeshttps://doi.org/10.1101/2020.02.04.934406openalex-snapshot
Discriminating changes in protein structure using PTAD conjugation to tyrosine
inferred← citeshttps://doi.org/10.1101/2022.08.12.22278659openalex-snapshot
Machine learning with validation to detect diabetic microvascular complications using clinical and metabolomics data
inferred← citeshttps://doi.org/10.1101/2024.01.07.574493openalex-snapshot
Effect of Pressure on the Conformational Landscape of Human γ D-crystallin from Replica Exchange Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1101/2025.03.11.642737openalex-snapshot
Unveiling Interaction Signatures Across Viral Pathogens through VASCO: Viral Antigen-Antibody Structural COmplex dataset
inferred← citeshttps://doi.org/10.1101/cshperspect.a032490openalex-snapshot
Beyond DNA and RNA: The Expanding Toolbox of Synthetic Genetics
inferred← citeshttps://doi.org/10.1111/imr.13439openalex-snapshot
The Evolving T Cell Receptor Recognition Code: The Rules Are More Like Guidelines
inferred← citeshttps://doi.org/10.1111/j.1600-065x.2012.01165.xopenalex-snapshot
Structural and dynamic control of T‐cell receptor specificity, cross‐reactivity, and binding mechanism
inferred← citeshttps://doi.org/10.1111/j.1742-4658.2011.08208.xopenalex-snapshot
Selection of a CXCR4 antagonist from a human heavy chain CDR3‐derived phage library
inferred← citeshttps://doi.org/10.1124/mol.113.088526openalex-snapshot
Pore-Exposed Tyrosine Residues of P-Glycoprotein Are Important Hydrogen-Bonding Partners for Drugs
inferred← citeshttps://doi.org/10.1126/sciadv.adk8157openalex-snapshot
Combinatorially restricted computational design of protein-protein interfaces to produce IgG heterodimers
inferred← citeshttps://doi.org/10.1126/sciimmunol.aaf7962openalex-snapshot
Conservation and diversity in the ultralong third heavy-chain complementarity-determining region of bovine antibodies
inferred← citeshttps://doi.org/10.1128/jb.01967-12openalex-snapshot
A Novel C-Terminal Region within the Multicargo Type III Secretion Chaperone CesT Contributes to Effector Secretion
inferred← citeshttps://doi.org/10.1128/jvi.01707-14openalex-snapshot
Probing the Functions of the Paramyxovirus Glycoproteins F and HN with a Panel of Synthetic Antibodies
inferred← citeshttps://doi.org/10.1152/ajpcell.00238.2014openalex-snapshot
Identification of Tyr residues that enhance folate substrate binding and constrain oscillation of the proton-coupled folate transporter (PCFT-SLC46A1)
inferred← citeshttps://doi.org/10.1186/1471-2105-14-s7-s9openalex-snapshot
Identification and analysis of conserved pockets on protein surfaces
inferred← citeshttps://doi.org/10.1186/1745-7580-6-s1-s1openalex-snapshot
Stacking and energetic contribution of aromatic islands at the binding interface of antibody proteins
inferred← citeshttps://doi.org/10.1201/b19023-12openalex-snapshot
Best Practices in Assessing the Developability of Biopharmaceutical Candidates
inferred← citeshttps://doi.org/10.1371/journal.pone.0055617openalex-snapshot
Protein Engineering with Biosynthesized Libraries from Bordetella bronchiseptica Bacteriophage
inferred← citeshttps://doi.org/10.1371/journal.pone.0076834openalex-snapshot
A Novel Heavy Domain Antibody Library with Functionally Optimized Complementarity Determining Regions
inferred← citeshttps://doi.org/10.1371/journal.pone.0082675openalex-snapshot
Tentative Identification of the Second Substrate Binding Site in Arabidopsis Phytochelatin Synthase
inferred← citeshttps://doi.org/10.1371/journal.pone.0086088openalex-snapshot
Encoding Asymmetry of the N-Glycosylation Motif Facilitates Glycoprotein Evolution
inferred← citeshttps://doi.org/10.1371/journal.pone.0104520openalex-snapshot
The Impact of Nitration on the Structure and Immunogenicity of the Major Birch Pollen Allergen Bet v 1.0101
inferred← citeshttps://doi.org/10.1371/journal.pone.0114610openalex-snapshot
Structure-Affinity Properties of a High-Affinity Ligand of FKBP12 Studied by Molecular Simulations of a Binding Intermediate
inferred← citeshttps://doi.org/10.1371/journal.pone.0138956openalex-snapshot
High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains
inferred← citeshttps://doi.org/10.1371/journal.pone.0316321openalex-snapshot
Site-selective photo-crosslinking for the characterisation of transient ubiquitin-like protein-protein interactions
inferred← citeshttps://doi.org/10.14429/dlsj.5.15999openalex-snapshot
Molecular Docking Unmasks Potent Phytoligands against SARS CoV 2 Spike Glycoprotein, Main Protease, Papain like Protease and RNA dependent RNA Polymerase
inferred← citeshttps://doi.org/10.18632/oncotarget.28469openalex-snapshot
Targeting Ras with protein engineering
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2609957/v1openalex-snapshot
Rapid screening methods for universal binding peptide aptamers against SARS-CoV-2 variant spikes, including omicron variants, and their application to diagnostic and therapeutic agents.
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2609957/v2openalex-snapshot
Rapid screening methods for universal binding peptide aptamers against SARS-CoV-2 variant spikes, including omicron variants, and their application to diagnostic and therapeutic agents.
inferred← citeshttps://doi.org/10.21203/rs.3.rs-9790437/v1openalex-snapshot
Empirical substitution models of SARS-CoV-2 protein evolution for phylogenetic inference
inferred← citeshttps://doi.org/10.2174/2210289201102010028openalex-snapshot
Synthesis of a Novel Class of Phosphonoaziridines as Interesting Antibacterial Agents
inferred← citeshttps://doi.org/10.2197/ipsjtbio.17.10openalex-snapshot
Exploring The Interplay Between Scoring Functions and Physico-chemical Properties in Antibody-antigen Docking
inferred← citeshttps://doi.org/10.22541/au.167101052.24746048/v1openalex-snapshot
Three types of hotspots- weak, moderate and strong in protein-protein and protein-peptide interactions
inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-tvgn1openalex-snapshot
Covalent Protein Inhibitors via Tyrosine Conjugation with Cyclic Imine Mannich Electrophiles
inferred← citeshttps://doi.org/10.3109/10409238.2011.609295openalex-snapshot
Structural anatomy of telomere OB proteins
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.339openalex-snapshot
Silica Polypeptide-Based Colloids: Physical Properties and Novel Materials
inferred← citeshttps://doi.org/10.32657/10356/58910openalex-snapshot
Novel methods and screens for portein stability engineering
inferred← citeshttps://doi.org/10.3389/fimmu.2012.00342openalex-snapshot
Natural and man-made V-gene repertoires for antibody discovery
inferred← citeshttps://doi.org/10.3389/fimmu.2020.570018openalex-snapshot
Blocking of the High-Affinity Interaction-Synapse Between SARS-CoV-2 Spike and Human ACE2 Proteins Likely Requires Multiple High-Affinity Antibodies: An Immune Perspective
inferred← citeshttps://doi.org/10.3389/fimmu.2021.702074openalex-snapshot
B Cell Mobilization, Dissemination, Fine Tuning of Local Antigen Specificity and Isotype Selection in Asthma
inferred← citeshttps://doi.org/10.3389/fimmu.2024.1359169openalex-snapshot
Unraveling the chicken T cell repertoire with enhanced genome annotation
inferred← citeshttps://doi.org/10.3389/fmolb.2021.639166openalex-snapshot
Shark Antibody Variable Domains Rigidify Upon Affinity Maturation—Understanding the Potential of Shark Immunoglobulins as Therapeutics
inferred← citeshttps://doi.org/10.3389/fnmol.2023.1322750openalex-snapshot
Delving into the significance of the His289Tyr single-nucleotide polymorphism in the glutamate ionotropic receptor kainate-1 (Grik1) gene of a genetically audiogenic seizure model
inferred← citeshttps://doi.org/10.3389/fnume.2023.1271208openalex-snapshot
Mini review of first-in-human integrin αvβ6 PET tracers
inferred← citeshttps://doi.org/10.3389/fphys.2014.00160openalex-snapshot
Principles of agonist recognition in Cys-loop receptors
inferred← citeshttps://doi.org/10.3390/biologics4040026openalex-snapshot
Selection and Characterization of Antibodies Recognizing Unnatural Base Pairs
inferred← citeshttps://doi.org/10.3390/biom11101437openalex-snapshot
Performance of Affinity-Improved DARPin Targeting HIV Capsid Domain in Interference of Viral Progeny Production
inferred← citeshttps://doi.org/10.3390/catal11091032openalex-snapshot
Role of PhOH and Tyrosine in Selective Oxidation of Hydrocarbons
inferred← citeshttps://doi.org/10.3390/chemosensors10100381openalex-snapshot
An AIEE Active Anthracene-Based Nanoprobe for Zn2+ and Tyrosine Detection Validated by Bioimaging Studies
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