Optimizing the affinity and specificity of proteins with molecular display.

Affinity maturation of receptor-ligand interactions represents an important area of academic and pharmaceutical research. Improving affinity and specificity of proteins can tailor potency for both in vivo and in vitro applications. A number of different display platforms including phage display, bacterial and yeast display, ribosome display, and mRNA display can optimize protein affinity and specificity. Here, we will review the advantages and disadvantages of these molecular display methods with a focus on their suitability for protein affinity maturation.

[1]  G. Georgiou,et al.  In vitro scanning saturation mutagenesis of an antibody binding pocket. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[2]  K. D. Hardman,et al.  Single-chain antigen-binding proteins. , 1988, Science.

[3]  Richard W Roberts,et al.  mRNA display: ligand discovery, interaction analysis and beyond. , 2003, Trends in biochemical sciences.

[4]  Peter Bohlen,et al.  Tailoring in Vitro Selection for a Picomolar Affinity Human Antibody Directed against Vascular Endothelial Growth Factor Receptor 2 for Enhanced Neutralizing Activity* , 2003, Journal of Biological Chemistry.

[5]  M. Teresa Pisabarro,et al.  Analysis of PDZ Domain-Ligand Interactions Using Carboxyl-terminal Phage Display* , 2000, The Journal of Biological Chemistry.

[6]  Anthony D. Keefe,et al.  The use of mRNA display to select high-affinity protein-binding peptides , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[7]  H. Steven Wiley,et al.  Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library , 2003, Nature Biotechnology.

[8]  Anthony D. Keefe,et al.  Functional proteins from a random-sequence library , 2001, Nature.

[9]  K. Wittrup,et al.  Fine Affinity Discrimination by Yeast Surface Display and Flow Cytometry , 2000, Biotechnology progress.

[10]  D. M. Brown,et al.  An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. , 1996, Journal of molecular biology.

[11]  David M. Kranz,et al.  TCRs with high affinity for foreign pMHC show self-reactivity , 2003, Nature Immunology.

[12]  Beat Ernst,et al.  Drug discovery today. , 2003, Current topics in medicinal chemistry.

[13]  W. Dower,et al.  An in vitro polysome display system for identifying ligands from very large peptide libraries. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[14]  J. Wells,et al.  Additivity of mutational effects in proteins. , 1990, Biochemistry.

[15]  H. Lowman,et al.  Affinity maturation of human growth hormone by monovalent phage display. , 1993, Journal of molecular biology.

[16]  Rapid evolution of peptide and protein binding properties in vitro. , 1992 .

[17]  V. Roschke,et al.  Discovery of high‐affinity peptide binders to BLyS by phage display , 2005, Journal of molecular recognition : JMR.

[18]  V. Quintero-Hernández,et al.  Directed evolution, phage display and combination of evolved mutants: a strategy to recover the neutralization properties of the scFv version of BCF2 a neutralizing monoclonal antibody specific to scorpion toxin Cn2. , 2005, Journal of molecular biology.

[19]  G. P. Smith,et al.  Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. , 1985, Science.

[20]  G. Georgiou,et al.  Quantitative analysis of the effect of the mutation frequency on the affinity maturation of single chain Fv antibodies. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[21]  G. Georgiou,et al.  Transport and anchoring of beta-lactamase to the external surface of Escherichia coli. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Christos Stathopoulos,et al.  Display of heterologous proteins on the surface of microorganisms: From the screening of combinatorial libraries to live recombinant vaccines , 1997, Nature Biotechnology.

[23]  G. Georgiou,et al.  Practical applications of engineering gram-negative bacterial cell surfaces. , 1993, Trends in biotechnology.

[24]  Y. Iba,et al.  Changes in the specificity of antibodies against steroid antigens by introduction of mutations into complementarity-determining regions of the V(H) domain. , 1998, Protein engineering.

[25]  Aaron Klug,et al.  In vivo repression by a site-specific DNA-binding protein designed against an oncogenic sequence , 1994, Nature.

[26]  D. Lauffenburger,et al.  Interleukin‐2 mutants with enhanced α‐receptor subunit binding affinity , 2003 .

[27]  P W Mansell,et al.  Pharmacokinetics of recombinant interleukin 2 in humans. , 1990, Cancer research.

[28]  T. Lövgren,et al.  Expanding the conformational diversity by random insertions to CDRH2 results in improved anti-estradiol antibodies. , 1999, Journal of molecular biology.

[29]  H R Hoogenboom,et al.  Multi-subunit proteins on the surface of filamentous phage: methodologies for displaying antibody (Fab) heavy and light chains. , 1991, Nucleic acids research.

[30]  C. Barbas,et al.  Building zinc fingers by selection: toward a therapeutic application. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[31]  R. Begent,et al.  Directed evolution of an anti-carcinoembryonic antigen scFv with a 4-day monovalent dissociation half-time at 37°C , 2004 .

[32]  G. Georgiou,et al.  Antibody affinity maturation using bacterial surface display. , 1998, Protein engineering.

[33]  G. Winter,et al.  Selection of phage antibodies by binding affinity. Mimicking affinity maturation. , 1992, Journal of molecular biology.

[34]  Baltazar Becerril,et al.  A strategy for the generation of specific human antibodies by directed evolution and phage display , 2005, The FEBS journal.

[35]  George Georgiou,et al.  Protection against anthrax toxin by recombinant antibody fragments correlates with antigen affinity , 2002, Nature Biotechnology.

[36]  A. Klug,et al.  A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter , 2001, Nature Biotechnology.

[37]  K. Wittrup,et al.  Biosynthetic polypeptide libraries. , 1999, Current opinion in biotechnology.

[38]  Andreas Plückthun,et al.  Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display , 2000, Nature Biotechnology.

[39]  Xie Hong-kun,et al.  Nature of Science , 2002 .

[40]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[41]  J. Foote,et al.  Breaking the affinity ceiling for antibodies and T cell receptors. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[42]  J. Wells,et al.  Growth hormone binding affinity for its receptor surpasses the requirements for cellular activity. , 1999, Biochemistry.

[43]  Y. Iba,et al.  Changes in the specificity of antibodies by site-specific mutagenesis followed by random mutagenesis. , 1999, Protein engineering.

[44]  Andreas Plückthun,et al.  Engineered proteins as specific binding reagents. , 2005, Current opinion in biotechnology.

[45]  Sachdev S Sidhu,et al.  Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis. , 2002, Journal of molecular biology.

[46]  J W Szostak,et al.  RNA-peptide fusions for the in vitro selection of peptides and proteins. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[47]  A. Plückthun,et al.  In vitro display technologies: novel developments and applications. , 2001, Current opinion in biotechnology.

[48]  Meir Glick,et al.  Stable, soluble T-cell receptor molecules for crystallization and therapeutics. , 2003, Protein engineering.

[49]  M. Saraste,et al.  FEBS Lett , 2000 .

[50]  Yi Li,et al.  Directed evolution of human T-cell receptors with picomolar affinities by phage display , 2005, Nature Biotechnology.

[51]  S. Deutscher,et al.  Identification of peptide sequences that bind the Thomsen-Friedenreich cancer-associated glycoantigen from bacteriophage peptide display libraries , 1996, Molecular Diversity.

[52]  N. Doi,et al.  STABLE: protein‐DNA fusion system for screening of combinatorial protein libraries in vitro , 1999, FEBS letters.

[53]  Robert Charles Ladner,et al.  Affinity maturation of Fab antibody fragments by fluorescent‐activated cell sorting of yeast‐displayed libraries , 2003, FEBS letters.

[54]  Paul H. Bessette,et al.  Rapid isolation of high-affinity protein binding peptides using bacterial display. , 2004, Protein engineering, design & selection : PEDS.

[55]  Guido Cappuccilli,et al.  A general method for greatly improving the affinity of antibodies by using combinatorial libraries. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[56]  T. Clackson,et al.  In vitro selection from protein and peptide libraries. , 1994, Trends in biotechnology.

[57]  J. Wells,et al.  Structural and mutational analysis of affinity-inert contact residues at the growth hormone-receptor interface. , 1996, Biochemistry.

[58]  Andreas Plückthun,et al.  In-vitro protein evolution by ribosome display and mRNA display. , 2004, Journal of immunological methods.

[59]  R. Siegel,et al.  Yeast mating for combinatorial Fab library generation and surface display , 2004, FEBS letters.

[60]  C. Glover,et al.  Gene expression profiling for hematopoietic cell culture , 2006 .

[61]  K D Wittrup,et al.  Optimal Screening of Surface‐Displayed Polypeptide Libraries , 1998, Biotechnology progress.

[62]  J. Bye,et al.  Isolation of high-affinity monomeric human anti-c-erbB-2 single chain Fv using affinity-driven selection. , 1996, Journal of molecular biology.

[63]  A. Plückthun,et al.  Directed in Vitro Evolution and Crystallographic Analysis of a Peptide-binding Single Chain Antibody Fragment (scFv) with Low Picomolar Affinity* , 2004, Journal of Biological Chemistry.

[64]  A. Plückthun,et al.  In vitro selection and evolution of functional proteins by using ribosome display. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[65]  S. Sidhu,et al.  Phage display for selection of novel binding peptides. , 2000, Methods in enzymology.

[66]  W. Stemmer.  Rapid evolution of a protein in vitro by DNA shuffling , 1994, Nature.

[67]  A. Plückthun,et al.  Ribosome display: an in vitro method for selection and evolution of antibodies from libraries. , 1999, Journal of immunological methods.

[68]  Erinna F. Lee,et al.  Affinity Maturation of Leukemia Inhibitory Factor and Conversion to Potent Antagonists of Signaling* , 2004, Journal of Biological Chemistry.

[69]  K Dane Wittrup,et al.  Development of a human light chain variable domain (V(L)) intracellular antibody specific for the amino terminus of huntingtin via yeast surface display. , 2004, Journal of molecular biology.

[70]  Matthew R. Clutter,et al.  High-affinity, peptide-specific T cell receptors can be generated by mutations in CDR1, CDR2 or CDR3. , 2005, Journal of molecular biology.

[71]  K D Wittrup,et al.  High affinity T cell receptors from yeast display libraries block T cell activation by superantigens. , 2001, Journal of molecular biology.

[72]  M. Little,et al.  Bacterial surface presentation of proteins and peptides: an alternative to phage technology? , 1993, Trends in biotechnology.

[73]  A. Plückthun,et al.  Tailoring in vitro evolution for protein affinity or stability. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[74]  K D Wittrup,et al.  Isolation of anti-T cell receptor scFv mutants by yeast surface display. , 1997, Protein engineering.

[75]  Noreen R. Gonzales,et al.  In vitro affinity maturation of a specificity-determining region-grafted humanized anticarcinoma antibody: isolation and characterization of minimally immunogenic high-affinity variants. , 2003, Clinical cancer research : an official journal of the American Association for Cancer Research.

[76]  J. S. Sullivan,et al.  Genomic Structure of an Attenuated Quasi Species of HIV-1 from a Blood Transfusion Donor and Recipients , 1995, Science.

[77]  Gregory A Weiss,et al.  Dissecting the Engrailed homeodomain-DNA interaction by phage-displayed shotgun scanning. , 2004, Chemistry & biology.

[78]  C. Eigenbrot,et al.  High-affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold. , 2004, Journal of molecular biology.

[79]  A. Plückthun,et al.  Ribosome display efficiently selects and evolves high-affinity antibodies in vitro from immune libraries. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[80]  Mitchell Ho,et al.  In Vitro Antibody Evolution Targeting Germline Hot Spots to Increase Activity of an Anti-CD22 Immunotoxin* , 2005, Journal of Biological Chemistry.

[81]  M. Graille,et al.  Fine Tuning of the Specificity of an Anti-progesterone Antibody by First and Second Sphere Residue Engineering* , 2005, Journal of Biological Chemistry.

[82]  G. Georgiou,et al.  Production and fluorescence-activated cell sorting of Escherichia coli expressing a functional antibody fragment on the external surface. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[83]  G. Georgiou,et al.  Development of an optimized expression system for the screening of antibody libraries displayed on the Escherichia coli surface. , 1999, Protein engineering.

[84]  D. Lauffenburger,et al.  Interleukin 2 (IL-2) variants engineered for increased IL-2 receptor alpha-subunit affinity exhibit increased potency arising from a cell surface ligand reservoir effect. , 2004, Molecular pharmacology.

[85]  S. Deutscher,et al.  Characterization of peptides that bind the tumor-associated Thomsen-Friedenreich antigen selected from bacteriophage display libraries. , 1997, Journal of molecular biology.

[86]  G. Winter,et al.  Phage antibodies: filamentous phage displaying antibody variable domains , 1990, Nature.

[87]  Eric T. Boder,et al.  Yeast surface display for screening combinatorial polypeptide libraries , 1997, Nature Biotechnology.

[88]  G. Griffiths,et al.  Development of humanized antibodies as cancer therapeutics. , 2005, Methods.

[89]  D. White,et al.  Directed evolution of a protein: selection of potent neutrophil elastase inhibitors displayed on M13 fusion phage. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[90]  G. Adams,et al.  Isolation of picomolar affinity anti-c-erbB-2 single-chain Fv by molecular evolution of the complementarity determining regions in the center of the antibody binding site. , 1996, Journal of molecular biology.

[91]  G. Georgiou,et al.  In vitro scanning saturation mutagenesis of all the specificity determining residues in an antibody binding site. , 1999, Protein engineering.

[92]  S. Deutscher,et al.  Combinatorial Evolution of High-Affinity Peptides That Bind to the Thomsen-Friedenreich Carcinoma Antigen , 2003, Journal of protein chemistry.

[93]  Y Husimi,et al.  In vitro virus: Bonding of mRNA bearing puromycin at the 3′‐terminal end to the C‐terminal end of its encoded protein on the ribosome in vitro , 1997, FEBS letters.

[94]  K D Wittrup,et al.  Protein engineering by cell-surface display. , 2001, Current opinion in biotechnology.

[95]  A. Wehnert,et al.  Construction and diversification of yeast cell surface displayed libraries by yeast mating: application to the affinity maturation of Fab antibody fragments. , 2004, Gene.

[96]  F. Jurnak,et al.  EF-Tu binding peptides identified, dissected, and affinity optimized by phage display. , 2003, Chemistry & biology.

[97]  D. Burton,et al.  Molecular characterization of the circulating anti-HIV-1 gp120-specific B cell repertoire using antibody phage display libraries generated from pre-selected HIV-1 gp120 binding PBLs. , 2005, Journal of immunological methods.

[98]  R. Ladner,et al.  Phage display-derived peptides as therapeutic alternatives to antibodies. , 2004, Drug discovery today.

[99]  D. Robbins,et al.  PCR-based random mutagenesis using manganese and reduced dNTP concentration. , 1997, BioTechniques.

[100]  David W. Colby,et al.  Potent inhibition of huntingtin aggregation and cytotoxicity by a disulfide bond-free single-domain intracellular antibody. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[101]  W. Dower,et al.  In vitro selection as a powerful tool for the applied evolution of proteins and peptides. , 2002, Current opinion in chemical biology.

[102]  P. Lohse,et al.  cDNA–Protein Fusions: Covalent Protein–Gene Conjugates for the In Vitro Selection of Peptides and Proteins , 2001 .

[103]  A. Plückthun,et al.  High-affinity binders selected from designed ankyrin repeat protein libraries , 2004, Nature Biotechnology.

[104]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[105]  A. Lim,et al.  Directed evolution of high-affinity antibody mimics using mRNA display. , 2002, Chemistry & biology.

[106]  S. Bass,et al.  Selecting high-affinity binding proteins by monovalent phage display. , 1991, Biochemistry.

[107]  J. Scott,et al.  Searching for peptide ligands with an epitope library. , 1990, Science.

[108]  K. Kosik,et al.  The Erbin PDZ Domain Binds with High Affinity and Specificity to the Carboxyl Termini of δ-Catenin and ARVCF* , 2002, The Journal of Biological Chemistry.

[109]  Herren Wu,et al.  Tailor-made antibody therapeutics. , 2005, Methods.

[110]  K D Wittrup,et al.  Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[111]  B Tidor,et al.  Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody. , 2004, Journal of molecular biology.

[112]  Michele C. Kieke,et al.  A yeast surface display system for the discovery of ligands that trigger cell activation. , 1998, Journal of immunological methods.

[113]  K D Wittrup,et al.  In vitro evolution of a T cell receptor with high affinity for peptide/MHC. , 2000, Proceedings of the National Academy of Sciences of the United States of America.