Protein Engineering

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  Subject Areas on Research

  • 15N, 13C and 1H backbone resonance assignments of an artificially engineered TEM-1/PSE-4 class A β-lactamase chimera and its deconvoluted mutant. 
  • A critical analysis of computational protein design with sparse residue interaction graphs. 
  • A genomics approach to improve the analysis and design of strain selections. 
  • A glycoengineered anti-CD19 antibody with potent antibody-dependent cellular cytotoxicity activity in vitro and lymphoma growth inhibition in vivo. 
  • A highly parallel method for synthesizing DNA repeats enables the discovery of 'smart' protein polymers. 
  • A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. 
  • A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity. 
  • A nanoscale force probe for gauging intermolecular interactions. 
  • A rationally-designed chimeric KDM1A/KDM1B histone demethylase tower domain deletion mutant retaining enzymatic activity. 
  • A unified model for de novo design of elastin-like polypeptides with tunable inverse transition temperatures. 
  • Addressing cell-sourcing limitations with gene therapy. 
  • Algorithm for backrub motions in protein design. 
  • Algorithms for protein design. 
  • An efficient parallel algorithm for accelerating computational protein design. 
  • An engineered liver glycogen phosphorylase with AMP allosteric activation. 
  • An engineered vascular endothelial growth factor-activating transcription factor induces therapeutic angiogenesis in ApoE knockout mice with hindlimb ischemia. 
  • Analysis of allosteric signal transduction mechanisms in an engineered fluorescent maltose biosensor. 
  • Analysis of the structural properties of cAMP-responsive element-binding protein (CREB) and phosphorylated CREB. 
  • Anti-infective biomaterials with surface-decorated tachyplesin I. 
  • Antibody light-chain-restricted recognition of the site of immune pressure in the RV144 HIV-1 vaccine trial is phylogenetically conserved. 
  • Atomic force microscopy captures length phenotypes in single proteins. 
  • B-cell depletion in vitro and in vivo with an afucosylated anti-CD19 antibody. 
  • Backbone resonance assignments of an artificially engineered TEM-1/PSE-4 Class A β-lactamase chimera. 
  • Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein. 
  • BioWarehouse: a bioinformatics database warehouse toolkit. 
  • Bioinformatic design of A-kinase anchoring protein-in silico: a potent and selective peptide antagonist of type II protein kinase A anchoring. 
  • Biosynthesis of (S)-4-chloro-3-hydroxybutanoate ethyl using Escherichia coli co-expressing a novel NADH-dependent carbonyl reductase and a glucose dehydrogenase. 
  • C-terminal opening mimics 'inside-out' activation of integrin alpha5beta1. 
  • CD86 (B7-2) can function to drive MHC-restricted antigen-specific CTL responses in vivo. 
  • Cell-Specific Chemical Delivery Using a Selective Nitroreductase-Nitroaryl Pair. 
  • Comparative immunogenicity of HIV-1 gp160, gp140 and gp120 expressed by live attenuated newcastle disease virus vector. 
  • Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. 
  • Computational design of a biologically active enzyme. 
  • Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. 
  • Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5. 
  • Computational protein engineering. 
  • Construction and phenotypic characterization of HIV type 1 functional envelope clones of subtypes G and F. 
  • Construction of a catalytically active iron superoxide dismutase by rational protein design. 
  • Construction of a family of Cys2His2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design. 
  • Construction of a novel redox protein by rational design: conversion of a disulfide bridge into a mononuclear iron-sulfur center. 
  • Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry. 
  • Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin. 
  • Conversion of a maltose receptor into a zinc biosensor by computational design. 
  • Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. 
  • Design of a calcium-binding protein with desired structure in a cell adhesion molecule. 
  • Design of bioelectronic interfaces by exploiting hinge-bending motions in proteins. 
  • Design, expression, and immunogenicity of a soluble HIV trimeric envelope fragment adopting a prefusion gp41 configuration. 
  • Designing an extracellular matrix protein with enhanced mechanical stability. 
  • Digital switching of local arginine density in a genetically encoded self-assembled polypeptide nanoparticle controls cellular uptake. 
  • Direct force measurements of the streptavidin-biotin interaction. 
  • Direct observation of multimer stabilization in the mechanical unfolding pathway of a protein undergoing oligomerization. 
  • Directed evolution of a pyruvate aldolase to recognize a long chain acyl substrate. 
  • Directed evolution of subtilisin E in Bacillus subtilis to enhance total activity in aqueous dimethylformamide. 
  • Directed self-assembly of monodisperse phospholipid bilayer Nanodiscs with controlled size. 
  • Effect of genetic circular permutation near the active site on the activity and stability of an enzyme inhibitor. 
  • Effect of protein fusion on the transition temperature of an environmentally responsive elastin-like polypeptide: a role for surface hydrophobicity? 
  • Eliminating antibody polyreactivity through addition of N-linked glycosylation. 
  • Engineered Ribonucleoprotein Granules Inhibit Translation in Protocells. 
  • Engineered chimeric streptavidin tetramers as novel tools for bioseparations and drug delivery. 
  • Engineered leucine zippers show that hemiphosphorylated CREB complexes are transcriptionally active. 
  • Engineered recombinant peanut protein and heat-killed Listeria monocytogenes coadministration protects against peanut-induced anaphylaxis in a murine model. 
  • Engineered zinc finger-activating vascular endothelial growth factor transcription factor plasmid DNA induces therapeutic angiogenesis in rabbits with hindlimb ischemia. 
  • Engineering a BCR-ABL-activated caspase for the selective elimination of leukemic cells. 
  • Engineering a biospecific communication pathway between cells and electrodes. 
  • Engineering biofilms for biocatalysis. 
  • Engineering oxidative stability in human hemoglobin based on the Hb providence (βK82D) mutation and genetic cross-linking. 
  • Engineering protein stability and specificity using fluorous amino acids: the importance of packing effects. 
  • Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. 
  • Engineering the substrate specificity of Staphylococcus aureus Sortase A. The beta6/beta7 loop from SrtB confers NPQTN recognition to SrtA. 
  • Engineering, expression, purification, and characterization of stable clade A/B recombinant soluble heterotrimeric gp140 proteins. 
  • Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain. 
  • Enzyme redesign guided by cancer-derived IDH1 mutations. 
  • Epitope tagging for tracking elastin-like polypeptides. 
  • Facilitative glucose transporter Glut1 is actively excluded from rod outer segments. 
  • Fast gap-free enumeration of conformations and sequences for protein design. 
  • Found in translation: applications of protein and peptide molecular diversity. 
  • Founder's Award, Society for Biomaterials. Sixth World Biomaterials Congress 2000, Kamuela, HI,May 15-20, 2000. Really smart bioconjugates of smart polymers and receptor proteins. 
  • Gene targeting to the ROSA26 locus directed by engineered zinc finger nucleases. 
  • Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. 
  • Generation of high-affinity human antibodies by combining donor-derived and synthetic complementarity-determining-region diversity. 
  • Generation, characterization and crystallization of a highly active and stable cytochrome bc1 complex mutant from Rhodobacter sphaeroides. 
  • Genes restoring redox balance in fermentation-deficient E. coli NZN111. 
  • Genetic engineering of a single-chain antibody fragment for surface immobilization in an optical biosensor. 
  • Genetic engineering of a suboptimal islet graft with A20 preserves beta cell mass and function. 
  • Genetically Encoded Cholesterol-Modified Polypeptides. 
  • HIV-1 VACCINES. HIV-1 neutralizing antibodies induced by native-like envelope trimers. 
  • Highly active zinc-finger nucleases by extended modular assembly. 
  • Human interleukin-2 production in insect (Trichoplusia ni) larvae: effects and partial control of proteolysis. 
  • Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates. 
  • Improved energy bound accuracy enhances the efficiency of continuous protein design. 
  • Improved pruning algorithms and divide-and-conquer strategies for Dead-End Elimination, with application to protein design 
  • In mice with type 2 diabetes, a vascular endothelial growth factor (VEGF)-activating transcription factor modulates VEGF signaling and induces therapeutic angiogenesis after hindlimb ischemia. 
  • In situ growth of a PEG-like polymer from the C terminus of an intein fusion protein improves pharmacokinetics and tumor accumulation. 
  • Incorporation of low molecular weight molecules into alpha(2)-macroglobulin by nucleophilic exchange. 
  • Integration of cell-free protein coexpression with an enzyme-linked immunosorbent assay enables rapid analysis of protein-protein interactions directly from DNA. 
  • LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency. 
  • Light-Dependent Cytoplasmic Recruitment Enhances the Dynamic Range of a Nuclear Import Photoswitch. 
  • Light-inducible gene regulation with engineered zinc finger proteins. 
  • Light-inducible spatiotemporal control of gene activation by customizable zinc finger transcription factors. 
  • Local encoding of computationally designed enzyme activity. 
  • Maintenance of native-like protein dynamics may not be required for engineering functional proteins. 
  • Manipulation of ligand binding affinity by exploitation of conformational coupling. 
  • Mapping phenotypic landscapes using DNA micro-arrays. 
  • Mechanical and chemical unfolding of a single protein: a comparison. 
  • Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering. 
  • Metalloprotein design. 
  • Molecular biology in cardiology: recent developments and opportunities for clinical applications. 
  • Molecular engineering of proteins and polymers for targeting and intracellular delivery of therapeutics. 
  • Monoclonal antibody therapy of human gliomas: current status and future approaches. 
  • Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling. 
  • Multiplex-PCR-based recombination as a novel high-fidelity method for directed evolution. 
  • Mutagenesis of the phosphate-binding pocket of KDPG aldolase enhances selectivity for hydrophobic substrates. 
  • Nanomechanics of streptavidin hubs for molecular materials. 
  • Natural product glycosyltransferases: properties and applications. 
  • Neural circuits. Labeling of active neural circuits in vivo with designed calcium integrators. 
  • Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies. 
  • Nonlinear protein degradation and the function of genetic circuits. 
  • Novel disulfide engineering in human carbonic anhydrase II using the PAIRWISE side-chain geometry database. 
  • OSPREY Predicts Resistance Mutations Using Positive and Negative Computational Protein Design. 
  • Optogenetic photochemical control of designer K+ channels in mammalian neurons. 
  • Orthogonal site-specific protein modification by engineering reversible thiol protection mechanisms. 
  • Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies. 
  • Parallel Computational Protein Design. 
  • Parallel on-chip gene synthesis and application to optimization of protein expression. 
  • Periplasmic binding proteins: a versatile superfamily for protein engineering. 
  • Plug-and-Play Protein Modification Using Homology-Independent Universal Genome Engineering. 
  • Production of adrenergic receptors in yeast. 
  • Proprietary science, open science and the role of patent disclosure: the case of zinc-finger proteins. 
  • Protein design using continuous rotamers. 
  • Protein engineering and the development of generic biosensors. 
  • Protein engineering approaches to biomaterials design. 
  • Protein fabrication automation. 
  • Protein interfacial pocket engineering via coupled computational filtering and biological focusing criterion. 
  • Quantitation of protein-protein interactions by thermal stability shift analysis. 
  • RNA-guided gene activation by CRISPR-Cas9-based transcription factors. 
  • Rational design and generation of recombinant control reagents for bispecific antibodies through CDR mutagenesis. 
  • Rational design of a calcium-binding protein. 
  • Rational protein design: combining theory and experiment. 
  • Re-design of Rhodobacter sphaeroides dimethyl sulfoxide reductase. Enhancement of adenosine N1-oxide reductase activity. 
  • Re-engineered CD40 receptor enables potent pharmacological activation of dendritic-cell cancer vaccines in vivo. 
  • Red cell antigens as functional molecules and obstacles to transfusion. 
  • Reverse engineering of the giant muscle protein titin. 
  • Role of citrate and phosphate anions in the mechanism of iron(III) sequestration by ferric binding protein: kinetic studies of the formation of the holoprotein of wild-type FbpA and its engineered mutants. 
  • Runx2/Cbfa1-genetically engineered skeletal myoblasts mineralize collagen scaffolds in vitro. 
  • Single protein misfolding events captured by atomic force microscopy. 
  • Site-specific conjugation of a temperature-sensitive polymer to a genetically-engineered protein. 
  • Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo. 
  • Special issue on engineered DNA-binding proteins. 
  • Streptavidin-biotin binding energetics. 
  • Strongly binding cell-adhesive polypeptides of programmable valencies. 
  • Structural optimization of a "smart" doxorubicin-polypeptide conjugate for thermally targeted delivery to solid tumors. 
  • Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190. 
  • Structure-guided reprogramming of serine recombinase DNA sequence specificity. 
  • SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics. 
  • Synthesis and characterization of a ruthenium(II)-based redox conjugate for reagentless biosensing. 
  • Synthesis of programmable integrases. 
  • Targeted entry via somatostatin receptors using a novel modified retrovirus glycoprotein that delivers genes at levels comparable to those of wild-type viral glycoproteins. 
  • Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase. 
  • Targeting a genetically engineered elastin-like polypeptide to solid tumors by local hyperthermia. 
  • Temperature sensitive peptides: engineering hyperthermia-directed therapeutics. 
  • The Chimpanzee SIV Envelope Trimer: Structure and Deployment as an HIV Vaccine Template. 
  • The immunocytokine NHS-IL12 as a potential cancer therapeutic. 
  • Three amino acid substitutions in domain I of calmodulin prevent the activation of chicken smooth muscle myosin light chain kinase. 
  • Tumor-specific CD8+ T cells expressing interleukin-12 eradicate established cancers in lymphodepleted hosts. 
  • Visualization of synaptic inhibition with an optogenetic sensor developed by cell-free protein engineering automation. 
  • X-ray crystallographic studies of streptavidin mutants binding to biotin. 
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  Keywords of People

  • Bennett, Vann, George Barth Geller Distinguished Professor of Molecular Biology, Duke Cancer Institute
  • Erickson, Harold Paul, James B. Duke Distinguished Professor of Cell Biology, Cell Biology
  • Gong, Yiyang, Assistant Professor in the Department of Biomedical Engineering, Duke Science & Society
  • Hoffman, Brenton D., James L. and Elizabeth M. Vincent Associate Professor of Biomedical Engineering, Biomedical Engineering
  • Reddy, Timothy E, Associate Professor of Biostatistics & Bioinformatics, Molecular Genetics and Microbiology
  • Richardson, David C., Professor of Biochemistry, Biochemistry
  • Sampson, John Howard, Robert H., M.D. and Gloria Wilkins Professor of Neurosurgery, in the School of Medicine, Immunology
  • Soderling, Scott Haydn, George Barth Geller Distinguished Professor of Molecular Biology, Cell Biology
  • Yan, Hai, Henry S. Friedman Distinguished Professor of Neuro-Oncology in the School of Medicine, Pathology