pH‐selective mutagenesis of protein–protein interfaces: In silico design of therapeutic antibodies with prolonged half‐life
Identifieur interne : 002888 ( Main/Exploration ); précédent : 002887; suivant : 002889pH‐selective mutagenesis of protein–protein interfaces: In silico design of therapeutic antibodies with prolonged half‐life
Auteurs : Velin Z. Spassov [États-Unis] ; Lisa Yan [États-Unis]Source :
- Proteins: Structure, Function, and Bioinformatics [ 0887-3585 ] ; 2013-04.
English descriptors
- Teeft :
- Aevdw bmgel, Affinity, Alanine, Alanine scanning, Alanine scanning results, Backbone interactions, Binding, Binding affinity, Binding behavior, Binding energy, Binding interface, Binding partners, Binding profile, Binding profiles, Biol, Biol chem, Blue bars, Cancer cells, Charmm, Chem, Combinatorial problem, Comput chem, Computational, Computational protocol, Conformation, Conformational flexibility, Cumulative effect, Dielectric constants, Different solution, Discovery studio, Dmgmut, Electrostatic contribution, Electrostatic contributions, Electrostatic energy terms, Electrostatic interactions, Electrostatic term, Energy terms, Experimental data, Fcrn, Fractional protonation, Free energy, Free energy differences, Free energy terms, Full agreement, Good agreement, Histidine scanning, Homology, Homology model, Hotspot, Information table, Interface, Interface residues, Ionization, Ionization properties, Ligand binding, Lysosomal degradation, Mgel, Monoclonal antibodies, More mutations, Multiple protonation states, Murine, Murine fcrn, Mutagenesis, Mutant, Mutant structures, Mutation, Mutation energies, Mutation energy, Neonatal, Neonatal receptor, Neutral effect, Other hand, Other mutations, Phys chem, Possible states, Protein, Protein binding affinity, Protein complexes, Protein design, Protein engineering, Protein ionization, Protein stability, Protein therapeutics, Proton binding, Protonation, Protonation state, Receptor, Residue, Same approach, Scanning, Several types, Significant effect, Silico, Silico design, Silico predictions, Single mutations, Single protonation state, Spassov, Target antigen, Telesis court, Therapeutic antibodies, Titratable groups, Titratable residues, Titratible residues, Triple mutation, Turkey ovomucoid, Unbound, Unbound states, Wild type, Wiley periodicals.
Abstract
Understanding the effects of mutation on pH‐dependent protein binding affinity is important in protein design, especially in the area of protein therapeutics. We propose a novel method for fast in silico mutagenesis of protein–protein complexes to calculate the effect of mutation as a function of pH. The free energy differences between the wild type and mutants are evaluated from a molecular mechanics model, combined with calculations of the equilibria of proton binding. The predicted pH‐dependent energy profiles demonstrate excellent agreement with experimentally measured pH‐dependency of the effect of mutations on the dissociation constants for the complex of turkey ovomucoid third domain (OMTKY3) and proteinase B. The virtual scanning mutagenesis identifies all hotspots responsible for pH‐dependent binding of immunoglobulin G (IgG) to neonatal Fc receptor (FcRn) and the results support the current understanding of the salvage mechanism of the antibody by FcRn based on pH‐selective binding. The method can be used to select mutations that change the pH‐dependent binding profiles of proteins and guide the time consuming and expensive protein engineering experiments. As an application of this method, we propose a computational strategy to search for mutations that can alter the pH‐dependent binding behavior of IgG to FcRn with the aim of improving the half‐life of therapeutic antibodies in the target organism. © Proteins 2013. © 2012 Wiley Periodicals, Inc.
Url:
DOI: 10.1002/prot.24230
Affiliations:
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<term>Backbone interactions</term>
<term>Binding</term>
<term>Binding affinity</term>
<term>Binding behavior</term>
<term>Binding energy</term>
<term>Binding interface</term>
<term>Binding partners</term>
<term>Binding profile</term>
<term>Binding profiles</term>
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<term>Biol chem</term>
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<term>Discovery studio</term>
<term>Dmgmut</term>
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<term>Other mutations</term>
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<term>Protein engineering</term>
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<term>Protein therapeutics</term>
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<front><div type="abstract" xml:lang="en">Understanding the effects of mutation on pH‐dependent protein binding affinity is important in protein design, especially in the area of protein therapeutics. We propose a novel method for fast in silico mutagenesis of protein–protein complexes to calculate the effect of mutation as a function of pH. The free energy differences between the wild type and mutants are evaluated from a molecular mechanics model, combined with calculations of the equilibria of proton binding. The predicted pH‐dependent energy profiles demonstrate excellent agreement with experimentally measured pH‐dependency of the effect of mutations on the dissociation constants for the complex of turkey ovomucoid third domain (OMTKY3) and proteinase B. The virtual scanning mutagenesis identifies all hotspots responsible for pH‐dependent binding of immunoglobulin G (IgG) to neonatal Fc receptor (FcRn) and the results support the current understanding of the salvage mechanism of the antibody by FcRn based on pH‐selective binding. The method can be used to select mutations that change the pH‐dependent binding profiles of proteins and guide the time consuming and expensive protein engineering experiments. As an application of this method, we propose a computational strategy to search for mutations that can alter the pH‐dependent binding behavior of IgG to FcRn with the aim of improving the half‐life of therapeutic antibodies in the target organism. © Proteins 2013. © 2012 Wiley Periodicals, Inc.</div>
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