Protein Engineering
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Subject Areas on Research
- 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.
- 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.
- 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.
- 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.
- C-terminal opening mimics 'inside-out' activation of integrin alpha5beta1.
- 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.
- 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.
- 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 chimeric streptavidin tetramers as novel tools for bioseparations and drug delivery.
- 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 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 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.
- Found in translation: applications of protein and peptide molecular diversity.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Neural circuits. Labeling of active neural circuits in vivo with designed calcium integrators.
- 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.
- Periplasmic binding proteins: a versatile superfamily for protein engineering.
- Production of adrenergic receptors in yeast.
- Protein engineering and the development of generic biosensors.
- Protein fabrication automation.
- 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-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 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 B. Geller Professor for Research in Molecular Biology in the School of Medicine, Duke Cancer Institute
- Erickson, Harold Paul, James B. Duke Professor of Cell Biology, Biomedical Engineering
- Gong, Yiyang, Assistant Professor in the Department of Biomedical Engineering, Duke Science & Society
- Hoffman, Brenton D., Assistant Professor of Biomedical Engineering, Biomedical Engineering
- Reddy, Timothy E, Associate Professor of Biostatistics & Bioinformatics, Molecular Genetics and Microbiology
- Richardson, David C., Professor of Biochemistry, Duke Cancer Institute
- Sampson, John Howard, Robert H., M.D. and Gloria Wilkins Professor of Neurosurgery, in the School of Medicine, Immunology
- Soderling, Scott Haydn, Professor in Cell Biology, Cell Biology
- Yan, Hai, Henry S. Friedman Professor of Neuro-Oncology in the School of Medicine, Pathology