Previous studies tracking AMPA receptor (AMPAR) diffusion at synapses observed a large mobile ext... more Previous studies tracking AMPA receptor (AMPAR) diffusion at synapses observed a large mobile extrasynaptic AMPAR pool. Using super-resolution microscopy, we examined how fluorophore size and photostability affected AMPAR trafficking outside of, and within, postsynaptic densities (PSDs) from rats. Organic fluorescent dyes (» 4 nm), quantum dots, either small (» 10 nm diameter; sQDs) or big (>20 nm; bQDs), were coupled to AMPARs via different-sized linkers. We find that >90% of AMPARs labeled with fluorescent dyes or sQDs were diffusing in confined nanodomains in PSDs, which were stable for 15 min or longer. Less than 10% of sQD-AMPARs were extrasynaptic and highly mobile. In contrast, 5-10% of bQD-AMPARs were in PSDs and 90-95% were extrasynaptic as previously observed. Contrary to the hypothesis that AMPAR entry is limited by the occupancy of open PSD 'slots', our findings suggest that AMPARs rapidly enter stable 'nanodomains' in PSDs with lifetime >15 min, and do not accumulate in extrasynaptic membranes.
Because streptavidin is a homotetramer, it can bind multiple biotinylated ligands and cause targe... more Because streptavidin is a homotetramer, it can bind multiple biotinylated ligands and cause target aggregation. To allow biotin detection without clustering, we previously engineered monomeric streptavidin (mSA) that is structurally similar to a single streptavidin subunit. Introducing the S25H mutation near the binding site increases the biotin dissociation half-life t 1/2 to 83 minutes. The slowly dissociating mutant, mSA2, is useful in imaging studies because it allows stable labeling of biotinylated targets. We show that mSA2 conjugated with Alexa 488 binds biotinylated receptors on HEK293 with high specifi city, and bound mSA2-Alexa488 does not dissociate signifi cantly during an imaging study lasting 50 minutes. As a structural monomer, mSA2 can be fused to other proteins to create bifunctional molecules. We tested the use of mSA2 in proximity dependent biotinylation, in which mSA2 is fused to a peptide or a protein that binds a protein of interest (POI) and is used to recruit photoactivatable biotin (PA-biotin) to the target molecule. Once the resulting cluster of interacting proteins is subjected to UV-initiated distance-dependent biotinylation, subsequent affi nity purifi cation of biotinylated proteins on streptavidin beads can identify protein molecules that interact with POI. In addition to proteins that directly interact with the mSA2 fusion, mSA2 also induces biotinylation of other proteins that are associated through a series of noncovalent interactions. We show that mSA2 fused to an antibody recognition domain can be recruited to the kinase Erk-2 using a commercially available antibody and induce biotinylation of a known Erk-2 substrate, GST-Elk-1. Therefore, mSA2 can be used to implement proximity dependent biotinylation and detect transient enzyme-substrate interactions.
Applied Microbiology and Biotechnology, Apr 2, 2014
We recently reported the engineering of monomeric streptavidin (mSA) for use in monomeric detecti... more We recently reported the engineering of monomeric streptavidin (mSA) for use in monomeric detection of biotinylated ligands. Although mSA can be expressed functionally on the surface of mammalian cells and yeast, the molecule does not fold correctly when expressed in Escherichia coli. Refolding from inclusion bodies is cumbersome and yields a limited amount of purified protein. Improving the final yield should facilitate its use in biotechnology. We tested the expression and purification of mSA fused to GST, MBP, thioredoxin, and sumo tags to simplify its purification and improve the yield. The fusion proteins can be expressed solubly in E. coli and increase the yield by more than 20fold. Unmodified mSA can be obtained by proteolytically removing the fusion tag. Purified mSA can be immobilized on a solid matrix to purify biotinylated ligands. Together, expressing mSA as a fusion with a solubilization tag vastly simplifies its preparation and increases its usability in biotechnology.
Applied Microbiology and Biotechnology, Sep 22, 2013
Streptavidin and its homologs (together referred to as streptavidin) are widely used in molecular... more Streptavidin and its homologs (together referred to as streptavidin) are widely used in molecular science owing to their highly selective and stable interaction with biotin. Other factors also contribute to the popularity of the streptavidin-biotin system, including the stability of the protein and various chemical and enzymatic biotinylation methods available for use with different experimental designs. The technology has enjoyed a renaissance of a sort in recent years, as new streptavidin variants are engineered to complement native proteins and novel methods of introducing selective biotinylation are developed for in vitro and in vivo applications. There have been notable developments in the areas of catalysis, cell biology, and proteomics in addition to continued applications in the more established areas of detection, labeling and drug delivery. This review summarizes recent advances in streptavidin engineering and new applications based on the streptavidin-biotin interaction.
with specic help available everywhere you see the i O symbol. The following versions of software ... more with specic help available everywhere you see the i O symbol. The following versions of software and data (see references i O) were used in the production of this report:
Background:BAFF and APRIL are TNF superfamily members that bind both TACI and BCMA on B cells; BA... more Background:BAFF and APRIL are TNF superfamily members that bind both TACI and BCMA on B cells; BAFF also binds BAFF-R. Together, BAFF and APRIL support B cell development, differentiation, and survival. Their co-neutralization dramatically reduces B cell function, including antibody production, whereas inhibition of either BAFF or APRIL alone mediates relatively modest effects.Objectives:While CTLA-4-based therapeutics that block T cell costimulation provide safe and moderately effective T cell inhibition in many disease settings, and while B cell targeting therapies have demonstrated promising therapeutic potential, we postulate that improved, combined BAFF and APRIL inhibition, either alone or coupled with inhibition of T cell costimulation, will provide more effective and durable relief from severe B cell-related autoimmune diseases like SLE.Methods:We used our directed evolution platform to identify variant domains of the TNF family receptors TACI or BCMA that exhibit enhanced a...
Introduction: Checkpoint inhibition (CPI) has been shown to be an effective anti-tumor therapy, b... more Introduction: Checkpoint inhibition (CPI) has been shown to be an effective anti-tumor therapy, but CPI alone is frequently insufficient to control tumor growth, and costimulatory signals may also be required to produce clinically significant anti-tumor responses. PD1-PDL1 are established CPI targets and TMIGD2 is an inhibitory receptor expressed on T cells that is engaged by its cognate ligand HHLA2 on tumor cells, leading to inhibition of T cell responses. Novel biologics combining CD28 costimulation and CPI may yield promising tumor antigen-specific therapeutic candidates. Methods: Variants of CD86 with increased CD28 affinity were engineered using our directed evolution platform. PD1 and TMIGD2 variants were also engineered for increased affinity to PDL1 and HHLA2, respectively. Fusion proteins were generated including either PD1 or TMIGD2 domains, an effectorless Fc domain, and an engineered CD86 domain to generate proteins to provide target-dependent costimulation (TDC) and ev...
BAFF and APRIL are TNF superfamily members that form homo- and heteromultimers that bind TACI and... more BAFF and APRIL are TNF superfamily members that form homo- and heteromultimers that bind TACI and BCMA on B cells; BAFF also binds BAFF-R. BAFF and APRIL support B cell development, differentiation, and survival, particularly for plasmablasts and plasma cells, and play critical roles in the pathogenesis of B cell-related autoimmune diseases. In nonclinical models, inhibition of either BAFF or APRIL alone mediates relatively modest effects, whereas their co-neutralization dramatically reduces B cell function, including antibody production. Fc fusions of wild-type (WT) TACI (e.g. atacicept and telitacicept) target both BAFF and APRIL and have demonstrated promising clinical potential in e.g. systemic lupus erythematosus (SLE) and IgA nephropathy but have not yet clearly exhibited long-term and/or complete disease remissions.To generate a dual BAFF/APRIL antagonist with inhibitory activity superior to WT TACI and BCMA and with the potential to improve clinical outcomes in B cell-mediat...
L'invention concerne des proteines immunomodulatrices comprenant des variants de CD112 et des... more L'invention concerne des proteines immunomodulatrices comprenant des variants de CD112 et des acides nucleiques codant pour ces proteines. Les proteines immunomodulatrices selon l'invention presentent une utilite therapeutique pour diverses affections immunologiques et oncologiques. La presente invention concerne des compositions et des methodes de fabrication et d'utilisation de ces proteines.
Whether AMPA receptors (AMPARs) enter into neuronal synapses, by exocytosis from an internal pool... more Whether AMPA receptors (AMPARs) enter into neuronal synapses, by exocytosis from an internal pool, or by diffusion from an external membrane-bound pool, is hotly contested. 3D super-resolution fluorescent nanoscopy to measure the dynamics and placement of AMPAR is a powerful method for addressing this issue. However, probe size and accessibility to tightly packed spaces can be limiting. We have therefore labeled AMPARs with differently sized fluorophores: small organic fluorescent dyes (~ 4 nm), small quantum dots (sQD, ~10 nm in diameter), or big (commercial) quantum dots (bQD, ~ 20 nm in diameter). We then compared their diffusion rate, trajectories, and placement with respect to a postsynaptic density (PSD) protein, Homer 1c. Labeled with the small probes of sQDs or organic fluorophores, we find that AMPARs are located largely within PSDs (~73-93%), and generally reside in "nanodomains" with constrained diffusion. In contrast, when labeled with bQDs, only 5-10% of AMPAR...
Electron paramagnetic resonance (EPR) spectroscopy has proven to be an excellent tool for probing... more Electron paramagnetic resonance (EPR) spectroscopy has proven to be an excellent tool for probing local structure and dynamics in biological systems.
Because streptavidin is a homotetramer, it can bind multiple biotinylated ligands and cause targe... more Because streptavidin is a homotetramer, it can bind multiple biotinylated ligands and cause target aggregation. To allow biotin detection without clustering, we previously engineered monomeric streptavidin (mSA) that is structurally similar to a single streptavidin subunit. Introducing the S25H mutation near the binding site increases the biotin dissociation half-life t1/2 to 83 minutes. The slowly dissociating mutant, mSA2, is useful in imaging studies because it allows stable labeling of biotinylated targets. We show that mSA2 conjugated with Alexa 488 binds biotinylated receptors on HEK293 with high specificity, and bound mSA2–Alexa488 does not dissociate significantly during an imaging study lasting 50 minutes. As a structural monomer, mSA2 can be fused to other proteins to create bifunctional molecules. We tested the use of mSA2 in proximity dependent biotinylation, in which mSA2 is fused to a peptide or a protein that binds a protein of interest (POI) and is used to recruit ph...
The majority of proteins in the cell interact with other proteins as part of their natural functi... more The majority of proteins in the cell interact with other proteins as part of their natural function. Identifying the components of stable and transient protein complexes is therefore important to understand protein function. To this end, mass spectrometry (MS) can significantly accelerate the rate of discovery by analyzing complex protein mixtures through high resolution peptide sequencing. A critical step during MS analysis is sample preparation. The protein complex of interest needs to be separated from other cellular components, many of which are present in high abundance and interact nonspecifically with the target protein. We used monomeric streptavidin (mSA), which was recently designed in our lab, to achieve selective chemical biotinylation of the proteins that interact with a protein of interest. Biotinylation allows the interacting proteins to be subsequently purified on streptavidin beads utilizing well known streptavidin-biotin interaction. Since biotinylation is irrevers...
Applied Biochemistry and Biotechnology, Aug 19, 2015
Inteins are protein segments embedded in frame within a precursor sequence that catalyze a self-e... more Inteins are protein segments embedded in frame within a precursor sequence that catalyze a self-excision reaction and ligate the flanking sequences with a standard peptide bond. Split inteins are expressed as two separate polypeptide fragments and trans-splice upon subunit association. Split inteins have found use in biotechnology applications but their use in postsynthetic domain assembly in vivo has been limited to the ligation of two protein domains. Alternatively, they have been used to splice three domains and fragments in vitro. To further develop split intein-based applications in vivo, we have designed a cell-based assay for the postsynthetic splicing of three protein domains using orthogonal split inteins. Using naturally and artificially split inteins, NpuDnaE and SspDnaB, we show that a multidomain protein of 128 kDa can be assembled in Escherichia coli from individually expressed domains. In the current system, the main bottleneck in achieving high yield of tandem trans-spliced product appears to be the limited solubility of the SspDnaB precursors. Optimizing protein solubility should be important to achieve efficient combinatorial synthesis of protein domains in the cell.
Previous studies tracking AMPA receptor (AMPAR) diffusion at synapses observed a large mobile ext... more Previous studies tracking AMPA receptor (AMPAR) diffusion at synapses observed a large mobile extrasynaptic AMPAR pool. Using super-resolution microscopy, we examined how fluorophore size and photostability affected AMPAR trafficking outside of, and within, postsynaptic densities (PSDs) from rats. Organic fluorescent dyes (» 4 nm), quantum dots, either small (» 10 nm diameter; sQDs) or big (>20 nm; bQDs), were coupled to AMPARs via different-sized linkers. We find that >90% of AMPARs labeled with fluorescent dyes or sQDs were diffusing in confined nanodomains in PSDs, which were stable for 15 min or longer. Less than 10% of sQD-AMPARs were extrasynaptic and highly mobile. In contrast, 5-10% of bQD-AMPARs were in PSDs and 90-95% were extrasynaptic as previously observed. Contrary to the hypothesis that AMPAR entry is limited by the occupancy of open PSD 'slots', our findings suggest that AMPARs rapidly enter stable 'nanodomains' in PSDs with lifetime >15 min, and do not accumulate in extrasynaptic membranes.
Because streptavidin is a homotetramer, it can bind multiple biotinylated ligands and cause targe... more Because streptavidin is a homotetramer, it can bind multiple biotinylated ligands and cause target aggregation. To allow biotin detection without clustering, we previously engineered monomeric streptavidin (mSA) that is structurally similar to a single streptavidin subunit. Introducing the S25H mutation near the binding site increases the biotin dissociation half-life t 1/2 to 83 minutes. The slowly dissociating mutant, mSA2, is useful in imaging studies because it allows stable labeling of biotinylated targets. We show that mSA2 conjugated with Alexa 488 binds biotinylated receptors on HEK293 with high specifi city, and bound mSA2-Alexa488 does not dissociate signifi cantly during an imaging study lasting 50 minutes. As a structural monomer, mSA2 can be fused to other proteins to create bifunctional molecules. We tested the use of mSA2 in proximity dependent biotinylation, in which mSA2 is fused to a peptide or a protein that binds a protein of interest (POI) and is used to recruit photoactivatable biotin (PA-biotin) to the target molecule. Once the resulting cluster of interacting proteins is subjected to UV-initiated distance-dependent biotinylation, subsequent affi nity purifi cation of biotinylated proteins on streptavidin beads can identify protein molecules that interact with POI. In addition to proteins that directly interact with the mSA2 fusion, mSA2 also induces biotinylation of other proteins that are associated through a series of noncovalent interactions. We show that mSA2 fused to an antibody recognition domain can be recruited to the kinase Erk-2 using a commercially available antibody and induce biotinylation of a known Erk-2 substrate, GST-Elk-1. Therefore, mSA2 can be used to implement proximity dependent biotinylation and detect transient enzyme-substrate interactions.
Applied Microbiology and Biotechnology, Apr 2, 2014
We recently reported the engineering of monomeric streptavidin (mSA) for use in monomeric detecti... more We recently reported the engineering of monomeric streptavidin (mSA) for use in monomeric detection of biotinylated ligands. Although mSA can be expressed functionally on the surface of mammalian cells and yeast, the molecule does not fold correctly when expressed in Escherichia coli. Refolding from inclusion bodies is cumbersome and yields a limited amount of purified protein. Improving the final yield should facilitate its use in biotechnology. We tested the expression and purification of mSA fused to GST, MBP, thioredoxin, and sumo tags to simplify its purification and improve the yield. The fusion proteins can be expressed solubly in E. coli and increase the yield by more than 20fold. Unmodified mSA can be obtained by proteolytically removing the fusion tag. Purified mSA can be immobilized on a solid matrix to purify biotinylated ligands. Together, expressing mSA as a fusion with a solubilization tag vastly simplifies its preparation and increases its usability in biotechnology.
Applied Microbiology and Biotechnology, Sep 22, 2013
Streptavidin and its homologs (together referred to as streptavidin) are widely used in molecular... more Streptavidin and its homologs (together referred to as streptavidin) are widely used in molecular science owing to their highly selective and stable interaction with biotin. Other factors also contribute to the popularity of the streptavidin-biotin system, including the stability of the protein and various chemical and enzymatic biotinylation methods available for use with different experimental designs. The technology has enjoyed a renaissance of a sort in recent years, as new streptavidin variants are engineered to complement native proteins and novel methods of introducing selective biotinylation are developed for in vitro and in vivo applications. There have been notable developments in the areas of catalysis, cell biology, and proteomics in addition to continued applications in the more established areas of detection, labeling and drug delivery. This review summarizes recent advances in streptavidin engineering and new applications based on the streptavidin-biotin interaction.
with specic help available everywhere you see the i O symbol. The following versions of software ... more with specic help available everywhere you see the i O symbol. The following versions of software and data (see references i O) were used in the production of this report:
Background:BAFF and APRIL are TNF superfamily members that bind both TACI and BCMA on B cells; BA... more Background:BAFF and APRIL are TNF superfamily members that bind both TACI and BCMA on B cells; BAFF also binds BAFF-R. Together, BAFF and APRIL support B cell development, differentiation, and survival. Their co-neutralization dramatically reduces B cell function, including antibody production, whereas inhibition of either BAFF or APRIL alone mediates relatively modest effects.Objectives:While CTLA-4-based therapeutics that block T cell costimulation provide safe and moderately effective T cell inhibition in many disease settings, and while B cell targeting therapies have demonstrated promising therapeutic potential, we postulate that improved, combined BAFF and APRIL inhibition, either alone or coupled with inhibition of T cell costimulation, will provide more effective and durable relief from severe B cell-related autoimmune diseases like SLE.Methods:We used our directed evolution platform to identify variant domains of the TNF family receptors TACI or BCMA that exhibit enhanced a...
Introduction: Checkpoint inhibition (CPI) has been shown to be an effective anti-tumor therapy, b... more Introduction: Checkpoint inhibition (CPI) has been shown to be an effective anti-tumor therapy, but CPI alone is frequently insufficient to control tumor growth, and costimulatory signals may also be required to produce clinically significant anti-tumor responses. PD1-PDL1 are established CPI targets and TMIGD2 is an inhibitory receptor expressed on T cells that is engaged by its cognate ligand HHLA2 on tumor cells, leading to inhibition of T cell responses. Novel biologics combining CD28 costimulation and CPI may yield promising tumor antigen-specific therapeutic candidates. Methods: Variants of CD86 with increased CD28 affinity were engineered using our directed evolution platform. PD1 and TMIGD2 variants were also engineered for increased affinity to PDL1 and HHLA2, respectively. Fusion proteins were generated including either PD1 or TMIGD2 domains, an effectorless Fc domain, and an engineered CD86 domain to generate proteins to provide target-dependent costimulation (TDC) and ev...
BAFF and APRIL are TNF superfamily members that form homo- and heteromultimers that bind TACI and... more BAFF and APRIL are TNF superfamily members that form homo- and heteromultimers that bind TACI and BCMA on B cells; BAFF also binds BAFF-R. BAFF and APRIL support B cell development, differentiation, and survival, particularly for plasmablasts and plasma cells, and play critical roles in the pathogenesis of B cell-related autoimmune diseases. In nonclinical models, inhibition of either BAFF or APRIL alone mediates relatively modest effects, whereas their co-neutralization dramatically reduces B cell function, including antibody production. Fc fusions of wild-type (WT) TACI (e.g. atacicept and telitacicept) target both BAFF and APRIL and have demonstrated promising clinical potential in e.g. systemic lupus erythematosus (SLE) and IgA nephropathy but have not yet clearly exhibited long-term and/or complete disease remissions.To generate a dual BAFF/APRIL antagonist with inhibitory activity superior to WT TACI and BCMA and with the potential to improve clinical outcomes in B cell-mediat...
L'invention concerne des proteines immunomodulatrices comprenant des variants de CD112 et des... more L'invention concerne des proteines immunomodulatrices comprenant des variants de CD112 et des acides nucleiques codant pour ces proteines. Les proteines immunomodulatrices selon l'invention presentent une utilite therapeutique pour diverses affections immunologiques et oncologiques. La presente invention concerne des compositions et des methodes de fabrication et d'utilisation de ces proteines.
Whether AMPA receptors (AMPARs) enter into neuronal synapses, by exocytosis from an internal pool... more Whether AMPA receptors (AMPARs) enter into neuronal synapses, by exocytosis from an internal pool, or by diffusion from an external membrane-bound pool, is hotly contested. 3D super-resolution fluorescent nanoscopy to measure the dynamics and placement of AMPAR is a powerful method for addressing this issue. However, probe size and accessibility to tightly packed spaces can be limiting. We have therefore labeled AMPARs with differently sized fluorophores: small organic fluorescent dyes (~ 4 nm), small quantum dots (sQD, ~10 nm in diameter), or big (commercial) quantum dots (bQD, ~ 20 nm in diameter). We then compared their diffusion rate, trajectories, and placement with respect to a postsynaptic density (PSD) protein, Homer 1c. Labeled with the small probes of sQDs or organic fluorophores, we find that AMPARs are located largely within PSDs (~73-93%), and generally reside in "nanodomains" with constrained diffusion. In contrast, when labeled with bQDs, only 5-10% of AMPAR...
Electron paramagnetic resonance (EPR) spectroscopy has proven to be an excellent tool for probing... more Electron paramagnetic resonance (EPR) spectroscopy has proven to be an excellent tool for probing local structure and dynamics in biological systems.
Because streptavidin is a homotetramer, it can bind multiple biotinylated ligands and cause targe... more Because streptavidin is a homotetramer, it can bind multiple biotinylated ligands and cause target aggregation. To allow biotin detection without clustering, we previously engineered monomeric streptavidin (mSA) that is structurally similar to a single streptavidin subunit. Introducing the S25H mutation near the binding site increases the biotin dissociation half-life t1/2 to 83 minutes. The slowly dissociating mutant, mSA2, is useful in imaging studies because it allows stable labeling of biotinylated targets. We show that mSA2 conjugated with Alexa 488 binds biotinylated receptors on HEK293 with high specificity, and bound mSA2–Alexa488 does not dissociate significantly during an imaging study lasting 50 minutes. As a structural monomer, mSA2 can be fused to other proteins to create bifunctional molecules. We tested the use of mSA2 in proximity dependent biotinylation, in which mSA2 is fused to a peptide or a protein that binds a protein of interest (POI) and is used to recruit ph...
The majority of proteins in the cell interact with other proteins as part of their natural functi... more The majority of proteins in the cell interact with other proteins as part of their natural function. Identifying the components of stable and transient protein complexes is therefore important to understand protein function. To this end, mass spectrometry (MS) can significantly accelerate the rate of discovery by analyzing complex protein mixtures through high resolution peptide sequencing. A critical step during MS analysis is sample preparation. The protein complex of interest needs to be separated from other cellular components, many of which are present in high abundance and interact nonspecifically with the target protein. We used monomeric streptavidin (mSA), which was recently designed in our lab, to achieve selective chemical biotinylation of the proteins that interact with a protein of interest. Biotinylation allows the interacting proteins to be subsequently purified on streptavidin beads utilizing well known streptavidin-biotin interaction. Since biotinylation is irrevers...
Applied Biochemistry and Biotechnology, Aug 19, 2015
Inteins are protein segments embedded in frame within a precursor sequence that catalyze a self-e... more Inteins are protein segments embedded in frame within a precursor sequence that catalyze a self-excision reaction and ligate the flanking sequences with a standard peptide bond. Split inteins are expressed as two separate polypeptide fragments and trans-splice upon subunit association. Split inteins have found use in biotechnology applications but their use in postsynthetic domain assembly in vivo has been limited to the ligation of two protein domains. Alternatively, they have been used to splice three domains and fragments in vitro. To further develop split intein-based applications in vivo, we have designed a cell-based assay for the postsynthetic splicing of three protein domains using orthogonal split inteins. Using naturally and artificially split inteins, NpuDnaE and SspDnaB, we show that a multidomain protein of 128 kDa can be assembled in Escherichia coli from individually expressed domains. In the current system, the main bottleneck in achieving high yield of tandem trans-spliced product appears to be the limited solubility of the SspDnaB precursors. Optimizing protein solubility should be important to achieve efficient combinatorial synthesis of protein domains in the cell.
Uploads
Papers by Daniel Demonte