Co-reporter:Alana F. Ogata, Joshua M. Edgar, Sudipta Majumdar, Jeffrey S. Briggs, Shae V. Patterson, Ming X. Tan, Stephan T. Kudlacek, Christine A. Schneider, Gregory A. Weiss, and Reginald M. Penner
Analytical Chemistry 2017 Volume 89(Issue 2) pp:
Publication Date(Web):December 19, 2016
DOI:10.1021/acs.analchem.6b04840
The label-free detection of human serum albumin (HSA) in aqueous buffer is demonstrated using a simple, monolithic, two-electrode electrochemical biosensor. In this device, both millimeter-scale electrodes are coated with a thin layer of a composite containing M13 virus particles and the electronically conductive polymer poly(3,4-ethylenedioxy thiophene) or PEDOT. These virus particles, engineered to selectively bind HSA, serve as receptors in this biosensor. The resistance component of the electrical impedance, Zre, measured between these two electrodes provides electrical transduction of HSA binding to the virus-PEDOT film. The analysis of sample volumes as small as 50 μL is made possible using a microfluidic cell. Upon exposure to HSA, virus-PEDOT films show a prompt increase in Zre within 5 s and a stable Zre signal within 15 min. HSA concentrations in the range from 100 nM to 5 μM are detectable. Sensor-to-sensor reproducibility of the HSA measurement is characterized by a coefficient-of-variance (COV) ranging from 2% to 8% across this entire concentration range. In addition, virus-PEDOT sensors successfully detected HSA in synthetic urine solutions.
Co-reporter:Kaitlin M Pugliese, Gregory A Weiss
Current Opinion in Chemical Biology 2017 Volume 41(Volume 41) pp:
Publication Date(Web):1 December 2017
DOI:10.1016/j.cbpa.2017.10.005
•DNA polymerases must differentiate between closely related substrates in the cell.•These enzymes have a surprising tolerance for deoxynucleoside triphosphate analogs.•Experiments with analog substrates can provide mechanistic insight into mutagenesis.•Recent methods to study DNA polymerization with analog substrates will be discussed.DNA polymerases must discriminate the correct Watson–Crick base pair-forming deoxynucleoside triphosphate (dNTP) substrate from three other dNTPs and additional triphosphates found in the cell. The rarity of misincorporations in vivo, then, belies the high tolerance for dNTP analogs observed in vitro. Advances over the last 10 years in single-molecule fluorescence and electronic detection of dNTP analog incorporation enable exploration of the mechanism and limits to base discrimination by DNA polymerases. Such studies reveal transient motions of DNA polymerase during substrate recognition and mutagenesis in the context of erroneous dNTP incorporation that can lead to evolution and genetic disease. Further improvements in time resolution and noise reduction of single-molecule studies will uncover deeper mechanistic understanding of this critical, first step in evolution.Download high-res image (68KB)Download full-size image
Co-reporter:Luz M. Meneghini;Sarvind Tripathi;Marcus A. Woodworth;Sudipta Majumdar;Thomas L. Poulos
Molecular BioSystems (2005-Present) 2017 vol. 13(Issue 8) pp:1438-1447
Publication Date(Web):2017/07/25
DOI:10.1039/C7MB00163K
Membrane proteins (MPs) constitute a third of all proteomes, and contribute to a myriad of cellular functions including intercellular communication, nutrient transport and energy generation. For example, TonB-dependent transporters (TBDTs) in the outer membrane of Gram-negative bacteria play an essential role transporting iron and other nutrients into the bacterial cell. The inherently hydrophobic surfaces of MPs complicates protein expression, purification, and characterization. Thus, dissecting the functional contributions of individual amino acids or structural features through mutagenesis can be a challenging ordeal. Here, we apply a new approach for the expedited protein characterization of the TBDT ShuA from Shigella dysenteriae, and elucidate the protein's initial steps during heme-uptake. ShuA variants were displayed on the surface of an M13 bacteriophage as fusions to the P8 coat protein. Each ShuA variant was analyzed for its ability to display on the bacteriophage surface, and functionally bind to hemoglobin. This technique streamlines isolation of stable MP variants for rapid characterization of binding to various ligands. Site-directed mutagenesis studies targeting each extracellular loop region of ShuA demonstrate no specific extracellular loop is required for hemoglobin binding. Instead two residues, His420 and His86 mediate this interaction. The results identify a loop susceptible to antibody binding, and also a small molecule motif capable of disrupting ShuA from S. dysenteriae. The approach is generalizable to the dissection of other phage-displayed TBDTs and MPs.
Co-reporter:Joshua Britton, Colin L. Raston and Gregory A. Weiss
Chemical Communications 2016 vol. 52(Issue 66) pp:10159-10162
Publication Date(Web):19 Jul 2016
DOI:10.1039/C6CC04210D
A versatile enzyme immobilization strategy for thin film continuous flow processing is reported. Here, non-covalent and glutaraldehyde bioconjugation are used to immobilize enzymes on the surfaces of borosilicate reactors. This approach requires only ng of protein per reactor tube, with the stock protein solution readily recycled to sequentially coat >10 reactors. Confining reagents to thin films during immobilization reduced the amount of protein, piranha-cleaning solution, and other reagents by ∼96%. Through this technique, there was no loss of catalytic activity over 10 h processing. The results reported here combines the benefits of thin film flow processing with the mild conditions of biocatalysis.
Co-reporter:Amanda J. H. Gilliam; Joshua N. Smith; Dylan Flather; Kevin M. Johnston; Andrew M. Gansmiller; Dmitry A. Fishman; Joshua M. Edgar; Mark Balk; Sudipta Majumdar
Journal of Medicinal Chemistry 2016 Volume 59(Issue 8) pp:4019-4025
Publication Date(Web):March 24, 2016
DOI:10.1021/acs.jmedchem.5b01536
Caveolin-1 is a target for academic and pharmaceutical research due to its many cellular roles and associated diseases. We report peptide WL47 (1), a small, high-affinity, selective disrupter of caveolin-1 oligomers. Developed and optimized through screening and analysis of synthetic peptide libraries, ligand 1 has 7500-fold improved affinity compared to its T20 parent ligand and an 80% decrease in sequence length. Ligand 1 will permit targeted study of caveolin-1 function.
Co-reporter:Kritika Mohan and Gregory A. Weiss
ACS Chemical Biology 2016 Volume 11(Issue 5) pp:1167
Publication Date(Web):March 1, 2016
DOI:10.1021/acschembio.6b00060
Long fascinating to biologists, viruses offer nanometer-scale benchtops for building molecular-scale devices and materials. Viruses tolerate a wide range of chemical modifications including reaction conditions, pH values, and temperatures. Recent examples of nongenetic manipulation of viral surfaces have extended viruses into applications ranging from biomedical imaging, drug delivery, tissue regeneration, and biosensors to materials for catalysis and energy generation. Chemical reactions on the phage surface include both covalent and noncovalent modifications, including some applied in conjunction with genetic modifications. Here, we survey viruses chemically augmented with capabilities limited only by imagination.
Co-reporter:Joshua Britton;Jared W. Castle; Gregory A. Weiss; Colin L. Raston
Chemistry - A European Journal 2016 Volume 22( Issue 31) pp:10773-10776
Publication Date(Web):
DOI:10.1002/chem.201602373
Abstract
Inspired by nature's ability to construct complex molecules through sequential synthetic transformations, an assembly line synthesis of α-aminophosphonates has been developed. In this approach, simple starting materials are continuously fed through a thin-film reactor where the intermediates accrue molecular complexity as they progress through the flow system. Flow chemistry allows rapid multistep transformations to occur via reaction compartmentalization, an approach not amenable to using conventional flasks. Thin film processing can also access facile in situ solvent exchange to drive reaction efficiency, and through this method, α-aminophosphonate synthesis requires only 443 s residence time to produce 3.22 g h−1. Assembly-line synthesis allows unprecedented reaction flexibility and processing efficiency.
Co-reporter:Kaitlin M. Pugliese; O. Tolga Gul; Yongki Choi; Tivoli J. Olsen; Patrick C. Sims; Philip G. Collins
Journal of the American Chemical Society 2015 Volume 137(Issue 30) pp:9587-9594
Publication Date(Web):July 6, 2015
DOI:10.1021/jacs.5b02074
DNA polymerases exhibit a surprising tolerance for analogs of deoxyribonucleoside triphosphates (dNTPs), despite the enzymes’ highly evolved mechanisms for the specific recognition and discrimination of native dNTPs. Here, individual DNA polymerase I Klenow fragment (KF) molecules were tethered to a single-walled carbon nanotube field-effect transistor (SWCNT-FET) to investigate accommodation of dNTP analogs with single-molecule resolution. Each base incorporation accompanied a change in current with its duration defined by τclosed. Under Vmax conditions, the average time of τclosed was similar for all analog and native dNTPs (0.2 to 0.4 ms), indicating no kinetic impact on this step due to analog structure. Accordingly, the average rates of dNTP analog incorporation were largely determined by durations with no change in current defined by τopen, which includes molecular recognition of the incoming dNTP. All α-thio-dNTPs were incorporated more slowly, at 40 to 65% of the rate for the corresponding native dNTPs. During polymerization with 6-Cl-2APTP, 2-thio-dTTP, or 2-thio-dCTP, the nanocircuit uncovered an alternative conformation represented by positive current excursions that does not occur with native dNTPs. A model consistent with these results invokes rotations by the enzyme’s O-helix; this motion can test the stability of nascent base pairs using nonhydrophilic interactions and is allosterically coupled to charged residues near the site of SWCNT attachment. This model with two opposing O-helix motions differs from the previous report in which all current excursions were solely attributed to global enzyme closure and covalent-bond formation. The results suggest the enzyme applies a dynamic stability-checking mechanism for each nascent base pair.
Co-reporter:Maxim V. Akhterov, Yongki Choi, Tivoli J. Olsen, Patrick C. Sims, Mariam Iftikhar, O. Tolga Gul, Brad L. Corso, Gregory A. Weiss, and Philip G. Collins
ACS Chemical Biology 2015 Volume 10(Issue 6) pp:1495
Publication Date(Web):March 12, 2015
DOI:10.1021/cb500750v
Single-molecule techniques can monitor the kinetics of transitions between enzyme open and closed conformations, but such methods usually lack the resolution to observe the underlying transition pathway or intermediate conformational dynamics. We have used a 1 MHz bandwidth carbon nanotube transistor to electronically monitor single molecules of the enzyme T4 lysozyme as it processes substrate. An experimental resolution of 2 μs allowed the direct recording of lysozyme’s opening and closing transitions. Unexpectedly, both motions required 37 μs, on average. The distribution of transition durations was also independent of the enzyme’s state: either catalytic or nonproductive. The observation of smooth, continuous transitions suggests a concerted mechanism for glycoside hydrolysis with lysozyme’s two domains closing upon the polysaccharide substrate in its active site. We distinguish these smooth motions from a nonconcerted mechanism, observed in approximately 10% of lysozyme openings and closings, in which the enzyme pauses for an additional 40–140 μs in an intermediate, partially closed conformation. During intermediate forming events, the number of rate-limiting steps observed increases to four, consistent with four steps required in the stepwise, arrow-pushing mechanism. The formation of such intermediate conformations was again independent of the enzyme’s state. Taken together, the results suggest lysozyme operates as a Brownian motor. In this model, the enzyme traces a single pathway for closing and the reverse pathway for enzyme opening, regardless of its instantaneous catalytic productivity. The observed symmetry in enzyme opening and closing thus suggests that substrate translocation occurs while the enzyme is closed.
Co-reporter:K. Mohan and G. A. Weiss
Molecular BioSystems 2015 vol. 11(Issue 12) pp:3264-3272
Publication Date(Web):07 Oct 2015
DOI:10.1039/C5MB00511F
Specific detection of circulating tumor cells and characterization of their aggressiveness could improve cancer diagnostics and treatment. Metastasis results from such tumor cells, and causes the majority of cancer deaths. Chemically modified viruses could provide an inexpensive and efficient approach to detect tumor cells and quantitate their cell surface biomarkers. However, non-specific adhesion between the cell surface receptors and the virus surface presents a challenge. This report describes wrapping the virus surface with different PEG architectures, including as fusions to oligolysine, linkers, spacers and scaffolded ligands. The reported PEG wrappers can reduce by >75% the non-specific adhesion of phage to cell surfaces. Dynamic light scattering verified the non-covalent attachment by the reported wrappers as increased sizes of the virus particles. Further modifications resulted in specific detection of prostate cancer cells expressing PSMA, a key prostate cancer biomarker. The approach allowed quantification of PSMA levels on the cell surface, and could distinguish more aggressive forms of the disease.
Co-reporter:Dr. Tom Z. Yuan;Callum F. G. Ormonde;Stephan T. Kudlacek;Sameeran Kunche;Joshua N. Smith;William A. Brown;Kaitlin M. Pugliese;Dr. Tivoli J. Olsen;Mariam Iftikhar; Colin L. Raston; Gregory A. Weiss
ChemBioChem 2015 Volume 16( Issue 3) pp:393-396
Publication Date(Web):
DOI:10.1002/cbic.201402427
Abstract
Recombinant protein overexpression of large proteins in bacteria often results in insoluble and misfolded proteins directed to inclusion bodies. We report the application of shear stress in micrometer-wide, thin fluid films to refold boiled hen egg white lysozyme, recombinant hen egg white lysozyme, and recombinant caveolin-1. Furthermore, the approach allowed refolding of a much larger protein, cAMP-dependent protein kinase A (PKA). The reported methods require only minutes, which is more than 100 times faster than conventional overnight dialysis. This rapid refolding technique could significantly shorten times, lower costs, and reduce waste streams associated with protein expression for a wide range of industrial and research applications.
Co-reporter:Kritika Mohan, Gregory A. Weiss
Analytical Biochemistry 2014 Volume 453() pp:1-3
Publication Date(Web):15 May 2014
DOI:10.1016/j.ab.2014.02.025
Abstract
M13 bacteriophage display presents polypeptides as fusions to phage coat proteins. Such phage-displayed ligands offer useful reagents for biosensors. Here, we report a modified phage propagation protocol for the consistent and robust display of two different genetically encoded ligands on the major coat protein, P8. The results demonstrate that the phage surface reaches a saturation point for maximum peptide display.
Co-reporter:Yongki Choi, Tivoli J. Olsen, Patrick C. Sims, Issa S. Moody, Brad L. Corso, Mytrang N. Dang, Gregory A. Weiss, and Philip G. Collins
Nano Letters 2013 Volume 13(Issue 2) pp:625-631
Publication Date(Web):January 16, 2013
DOI:10.1021/nl304209p
Single-molecule experimental methods have provided new insights into biomolecular function, dynamic disorder, and transient states that are all invisible to conventional measurements. A novel, nonfluorescent single-molecule technique involves attaching single molecules to single-walled carbon nanotube field-effective transistors (SWNT FETs). These ultrasensitive electronic devices provide long-duration, label-free monitoring of biomolecules and their dynamic motions. However, generalization of the SWNT FET technique first requires design rules that can predict the success and applicability of these devices. Here, we report on the transduction mechanism linking enzymatic processivity to electrical signal generation by a SWNT FET. The interaction between SWNT FETs and the enzyme lysozyme was systematically dissected using eight different lysozyme variants synthesized by protein engineering. The data prove that effective signal generation can be accomplished using a single charged amino acid, when appropriately located, providing a foundation to widely apply SWNT FET sensitivity to other biomolecular systems.
Co-reporter:Kritika Mohan ; Keith C. Donavan ; Jessica A. Arter ; Reginald M. Penner
Journal of the American Chemical Society 2013 Volume 135(Issue 20) pp:7761-7767
Publication Date(Web):April 24, 2013
DOI:10.1021/ja4028082
The sensitive detection of cancer biomarkers in urine could revolutionize cancer diagnosis and treatment. Such detectors must be inexpensive, easy to interpret, and sensitive. This report describes a bioaffinity matrix of viruses integrated into PEDOT films for electrochemical sensing of prostate-specific membrane antigen (PSMA), a prostate cancer biomarker. High sensitivity to PSMA resulted from synergistic action by two different ligands to PSMA on the same phage particle. One ligand was genetically encoded, and the secondary recognition ligand was chemically synthesized to wrap around the phage. The dual ligands result in a bidentate binder with high-copy, dense ligand display for enhanced PSMA detection through a chelate-based avidity effect. Biosensing with virus–PEDOT films provides a 100 pM limit of detection for PSMA in synthetic urine without requiring enzymatic or other amplification.
Co-reporter:Patrick C. Sims ; Issa S. Moody ; Yongki Choi ; Chengjun Dong ; Mariam Iftikhar ; Brad L. Corso ; O. Tolga Gul ; Philip G. Collins
Journal of the American Chemical Society 2013 Volume 135(Issue 21) pp:7861-7868
Publication Date(Web):April 30, 2013
DOI:10.1021/ja311604j
Single-molecule studies of enzymes open a window into their dynamics and kinetics. A single molecule of the catalytic domain of cAMP-dependent protein kinase A (PKA) was attached to a single-walled carbon nanotube device for long-duration monitoring. The electronic recording clearly resolves substrate binding, ATP binding, and cooperative formation of PKA’s catalytically functional, ternary complex. Using recordings of a single PKA molecule extending over 10 min and tens of thousands of binding events, we determine the full transition probability matrix and conversion rates governing formation of the apo, intermediate, and closed enzyme configurations. We also observe kinetic rates varying over 2 orders of magnitude from one second to another. Anti-correlation of the on and off rates for PKA binding to the peptide substrate, but not ATP, demonstrates that regulation of enzyme activity results from altering the stability of the PKA–substrate complex, not its binding to ATP. The results depict a highly dynamic enzyme offering dramatic possibilities for regulated activity, an attribute useful for an enzyme with crucial roles in cell signaling.
Co-reporter:Tivoli J. Olsen ; Yongki Choi ; Patrick C. Sims ; O. Tolga Gul ; Brad L. Corso ; Chengjun Dong ; William A. Brown ; Philip G. Collins
Journal of the American Chemical Society 2013 Volume 135(Issue 21) pp:7855-7860
Publication Date(Web):April 30, 2013
DOI:10.1021/ja311603r
Bioconjugating single molecules of the Klenow fragment of DNA polymerase I into electronic nanocircuits allowed electrical recordings of enzymatic function and dynamic variability with the resolution of individual nucleotide incorporation events. Continuous recordings of DNA polymerase processing multiple homopolymeric DNA templates extended over 600 s and through >10 000 bond-forming events. An enzymatic processivity of 42 nucleotides for a template of the same length was directly observed. Statistical analysis determined key kinetic parameters for the enzyme’s open and closed conformations. Consistent with these nanocircuit-based observations, the enzyme’s closed complex forms a phosphodiester bond in a highly efficient process >99.8% of the time, with a mean duration of only 0.3 ms for all four dNTPs. The rate-limiting step for catalysis occurs during the enzyme’s open state, but with a nearly 2-fold longer duration for dATP or dTTP incorporation than for dCTP or dGTP into complementary, homopolymeric DNA templates. Taken together, the results provide a wealth of new information complementing prior work on the mechanism and dynamics of DNA polymerase I.
Co-reporter:Yongki Choi ; Issa S. Moody ; Patrick C. Sims ; Steven R. Hunt ; Brad L. Corso ; David E. Seitz ; Larry C. Blaszczak ; Philip G. Collins
Journal of the American Chemical Society 2012 Volume 134(Issue 4) pp:2032-2035
Publication Date(Web):January 9, 2012
DOI:10.1021/ja211540z
The dynamic processivity of individual T4 lysozyme molecules was monitored in the presence of either linear or cross-linked peptidoglycan substrates. Single-molecule monitoring was accomplished using a novel electronic technique in which lysozyme molecules were tethered to single-walled carbon nanotube field-effect transistors through pyrene linker molecules. The substrate-driven hinge-bending motions of lysozyme induced dynamic electronic signals in the underlying transistor, allowing long-term monitoring of the same molecule without the limitations of optical quenching or bleaching. For both substrates, lysozyme exhibited processive low turnover rates of 20–50 s–1 and rapid (200–400 s–1) nonproductive motions. The latter nonproductive binding events occupied 43% of the enzyme’s time in the presence of the cross-linked peptidoglycan but only 7% with the linear substrate. Furthermore, lysozyme catalyzed the hydrolysis of glycosidic bonds to the end of the linear substrate but appeared to sidestep the peptide cross-links to zigzag through the wild-type substrate.
Co-reporter:Jessica A. Arter, Juan E. Diaz, Keith C. Donavan, Tom Yuan, Reginald M. Penner, and Gregory A. Weiss
Analytical Chemistry 2012 Volume 84(Issue 6) pp:2776-2783
Publication Date(Web):February 17, 2012
DOI:10.1021/ac203143y
We demonstrate the de novo fabrication of a biosensor, based upon virus-containing poly(3,4-ethylene-dioxythiophene) (PEDOT) nanowires, that detects prostate-specific membrane antigen (PSMA). This development process occurs in three phases: (1) isolation of a M13 virus with a displayed polypeptide receptor, from a library of ≈1011 phage-displayed peptides, which binds PSMA with high affinity and selectivity, (2) microfabrication of PEDOT nanowires that entrain these virus particles using the lithographically patterned nanowire electrodeposition (LPNE) method, and (3) electrical detection of the PSMA in high ionic strength (150 mM salt) media, including synthetic urine, using an array of virus–PEDOT nanowires with the electrical resistance of these nanowires for transduction. The electrical resistance of an array of these nanowires increases linearly with the PSMA concentration from 20 to 120 nM in high ionic strength phosphate-buffered fluoride (PBF) buffer, yielding a limit of detection (LOD) for PSMA of 56 nM.
Co-reporter:Issa S. Moody, Shawn C. Verde, Cathie M. Overstreet, W. Edward Robinson Jr., Gregory A. Weiss
Bioorganic & Medicinal Chemistry Letters 2012 Volume 22(Issue 17) pp:5584-5589
Publication Date(Web):1 September 2012
DOI:10.1016/j.bmcl.2012.07.008
A protein without natural binding functions was engineered to bind HIV-1 integrase. Phage display selections applied a library of variants based on the C-terminal domain of the eye lens protein human γS-crystallin. Multiple loop regions were altered to encode libraries with ≈3.6 × 1011 different variants. A crystallin variant, termed integrase binding protein-10 (IBP-10), inhibits integrase catalysis with nanomolar Ki values. IBP-10 interacts with the integrase C-terminal domain and inhibits integrase substrate affinity. This allosteric mechanism allows IBP-10 to inhibit drug-resistant integrase variants. The results demonstrate the applicability of the crystallin scaffold for the discovery of binding partners and enzyme inhibitors.
Co-reporter:Keith C. Donavan, Jessica A. Arter, Gregory A. Weiss, and Reginald M. Penner
Langmuir 2012 Volume 28(Issue 34) pp:12581-12587
Publication Date(Web):August 2, 2012
DOI:10.1021/la302473j
Virus-poly(3,4-ethylenedioxythiophene) (virus-PEDOT) biocomposite films are prepared by electropolymerizing 3,4-ethylenedioxythiophene (EDOT) in aqueous electrolytes containing 12 mM LiClO4 and the bacteriophage M13. The concentration of virus in these solutions, [virus]soln, is varied from 3 to 15 nM. A quartz crystal microbalance is used to directly measure the total mass of the biocomposite film during its electrodeposition. In combination with a measurement of the electrodeposition charge, the mass of the virus incorporated into the film is calculated. These data show that the concentration of the M13 within the electropolymerized film, [virus]film, increases linearly with [virus]soln. The incorporation of virus particles into the PEDOT film from solution is efficient, resulting in a concentration ratio of [virus]film:[virus]soln ≈ 450. Virus incorporation into the PEDOT causes roughening of the film topography that is observed using scanning electron microscopy and atomic force microscopy (AFM). The electrical conductivity of the virus-PEDOT film, measured perpendicular to the plane of the film using conductive tip AFM, decreases linearly with virus loading, from 270 μS/cm for pure PEDOT films to 50 μS/cm for films containing 100 μM virus. The presence on the virus surface of displayed affinity peptides did not significantly influence the efficiency of incorporation into virus-PEDOT biocomposite films.
Co-reporter:Yongki Choi;Issa S. Moody;Patrick C. Sims;Steven R. Hunt;Brad L. Corso;Israel Perez;Philip G. Collins
Science 2012 Vol 335(6066) pp:319-324
Publication Date(Web):20 Jan 2012
DOI:10.1126/science.1214824
Co-reporter:Sudipta Majumdar ; Agnes Hajduczki ; Rosemarie Vithayathil ; Tivoli J. Olsen ; Ryan M. Spitler ; Aaron S. Mendez ; Travis D. Thompson
Journal of the American Chemical Society 2011 Volume 133(Issue 25) pp:9855-9862
Publication Date(Web):May 26, 2011
DOI:10.1021/ja201792q
Membrane proteins comprise a third of the human genome, yet present challenging targets for reverse chemical genetics. For example, although implicated in numerous diseases including multiple myeloma, the membrane protein caveolin-1 appears to offer a poor target for the discovery of synthetic ligands due to its largely unknown structure and insolubility. To break this impasse and identify new classes of caveolae controlling lead compounds, we applied phage-based, reverse chemical genetics for the discovery of caveolin-1 ligands derived from the anti-HIV therapeutic T20. Substitution of homologous residues into the T20 sequence used a process analogous to medicinal chemistry for the affinity maturation to bind caveolin. The resultant caveolin-1 ligands bound with >1000-fold higher affinity than wild-type T20. Two types of ELISAs and isothermal titration calorimetry (ITC) measurements demonstrated high affinity binding to caveolin by the T20 variants with Kd values in the 150 nM range. Microscopy experiments with the highest affinity caveolin ligands confirmed colocalization of the ligands with endogenous caveolin in NIH 3T3 cells. The results establish the foundation for targeting caveolin and caveolae formation in living cells.
Co-reporter:Agnes Hajduczki, Sudipta Majumdar, Marie Fricke, Isola A. M. Brown, and Gregory A. Weiss
ACS Chemical Biology 2011 Volume 6(Issue 4) pp:301
Publication Date(Web):December 30, 2010
DOI:10.1021/cb1001729
Hydrophobic and aggregation-prone, membrane proteins often prove too insoluble for conventional in vitro biochemical studies. To engineer soluble variants of human caveolin-1, a phage-displayed library of caveolin variants targeted the hydrophobic intramembrane domain with substitutions to charged residues. Anti-selections for insolubility removed hydrophobic variants, and positive selections for binding to the known caveolin ligand HIV gp41 isolated functional, folded variants. Assays with several caveolin binding partners demonstrated the successful folding and functionality by a solubilized, full-length caveolin variant selected from the library. This caveolin variant allowed assay of the direct interaction between caveolin and cavin. Clustered along one face of a putative helix, the solubilizing mutations suggest a structural model for the intramembrane domain of caveolin. The approach provides a potentially general method for solubilization and engineering of membrane-associated proteins by phage display.
Co-reporter:Glenn M. Eldridge and Gregory A. Weiss
Bioconjugate Chemistry 2011 Volume 22(Issue 10) pp:2143
Publication Date(Web):September 12, 2011
DOI:10.1021/bc200415v
New site-specific protein labeling (SSPL) reactions for targeting-specific, short peptides could be useful for the real-time detection of proteins inside of living cells. One SSPL approach matches bioorthogonal reagents with complementary peptides. Here, hydrazide reactive peptides were selected from phage-displayed libraries using reaction-based selections. Selection conditions included washes of varying pH and treatment with NaCNBH3 in order to specifically select reactive carbonyl-containing peptides. Selected peptides were fused to T4 lysozyme or synthesized on filter paper for colorimetric assays of the peptide–hydrazide interaction. A peptide–lysozyme protein fusion demonstrated specific, covalent labeling by the hydrazide reactive (HyRe) peptides in crude bacterial cell lysates, sufficient for the specific detection of an overexpressed protein fusion. Chemical synthesis of a short HyRe tag variant and subsequent reaction with two structurally distinct hydrazide probes produced covalent adducts observable by MALDI-TOF MS and MS/MS. Rather than isolating reactive carbonyl-containing peptides, we observed reaction with the N-terminal His of HyRe tag 114, amino acid sequence HKSNHSSKNRE, which attacks the hydrazide carbonyl at neutral pH. However, at the pH used during selection wash steps (<6.0), an alternative imine-containing product is formed that can be reduced with sodium cyanoborohydride. MSMS further reveals that this low pH product forms an adduct on Ser6. Further optimization of the novel bimolecular reaction described here could provide a useful tool for in vivo protein labeling and bioconjugate synthesis. The reported selection and screening methods could be widely applicable to the identification of peptides capable of other site-specific protein labeling reactions with bioorthogonal reagents.
Co-reporter:Jessica A. Arter, David K. Taggart, Theresa M. McIntire, Reginald M. Penner, and Gregory A. Weiss
Nano Letters 2010 Volume 10(Issue 12) pp:4858-4862
Publication Date(Web):November 1, 2010
DOI:10.1021/nl1025826
The separate fields of conducting polymer-based electrochemical sensors and virus-based molecular recognition offer numerous advantages for biosensing. Grafting M13 bacteriophage into an array of poly (3,4-ethylenedioxythiophene) (PEDOT) nanowires generated hybrids of conducting polymers and viruses. The virus incorporation into the polymeric backbone of PEDOT occurs during electropolymerization via lithographically patterned nanowire electrodeposition. The resultant arrays of virus-PEDOT nanowires enable real-time, reagent-free electrochemical biosensing of analytes in physiologically relevant buffers.
Co-reporter:Tilman Brück;Hans Hilgenkamp;Catherine Beaudry;Rees Kassen;Nitsara Karoonuthaisiri;Hiba Salah el Din Mohamed
Science 2010 Volume 329(Issue 5992) pp:626-627
Publication Date(Web):06 Aug 2010
DOI:10.1126/science.329.5992.626-b
Co-reporter:Jorge A. Lamboy ; Jessica A. Arter ; Kristeene A. Knopp ; Denise Der ; Cathie M. Overstreet ; Edmund F. Palermo ; Hiromitsu Urakami ; Ting-Bin Yu ; Ozgul Tezgel ; Gregory N. Tew ; Zhibin Guan ; Kenichi Kuroda
Journal of the American Chemical Society 2009 Volume 131(Issue 45) pp:16454-16460
Publication Date(Web):October 26, 2009
DOI:10.1021/ja9050873
M13 phage have provided scaffolds for nanostructure synthesis based upon self-assembled inorganic and hard materials interacting with phage-displayed peptides. Additionally, phage display has been used to identify binders to plastic, TiO2, and other surfaces. However, synthesis of phage-based materials through the hybridization of soft materials with the phage surface remains unexplored. Here, we present an efficient “phage wrapping” strategy for the facile synthesis of phage coated with soluble, cationic polymers. Polymers bearing high positive charge densities demonstrated the most effective phage wrapping, as shown by assays for blocking nonspecific binding of the anionic phage coat to a high pI target protein. The results establish the functional group requirements for hybridizing phage with soft materials and solve a major problem in phage display—nonspecific binding by the phage to high pI target proteins.
Co-reporter:Li-Mei C. Yang, Juan E. Diaz, Theresa M. McIntire, Gregory A. Weiss and Reginald M. Penner
Analytical Chemistry 2008 Volume 80(Issue 15) pp:5695
Publication Date(Web):July 1, 2008
DOI:10.1021/ac8008109
Electrochemical impedance spectroscopy is used to detect the binding of a 148.2 kDa antibody to a “covalent virus layer” (CVL) immobilized on a gold electrode. The CVL consisted of M13 phage particles covalently anchored to a 3 mm diameter gold disk electrode. The ability of the CVL to distinguish this antibody (“p-Ab”) from a second, nonbinding antibody (“n-Ab”) was evaluated as a function of the frequency and phase of the measured current relative to the applied voltage. The binding of p-Ab to the CVL was correlated with a change in the resistance, reducing it at low frequency (1−40 Hz) while increasing it at high frequency (2−140 kHz). The capacitance of the CVL was virtually uncorrelated with p-Ab binding. At both low and high frequency, the electrode resistance was linearly dependent on the p-Ab concentration from 20 to 266 nM but noise compromised the reproducibility of the p-Ab measurement at frequencies below 40 Hz. A “signal-to-noise” ratio for antibody detection was computed based upon the ratio between the measured resistance change upon p-Ab binding and the standard deviation of this change obtained from multiple measurements. In spite of the fact that the impedance change upon p-Ab binding in the low frequency domain was more than 100 times larger than that measured at high frequency, the S/N ratio at high frequency was higher and virtually independent of frequency from 4 to 140 kHz. Attempts to release p-Ab from the CVL using 0.05 M HCl, as previously described for mass-based detection, caused a loss of sensitivity that may be associated with a transition of these phage particles within the CVL from a linear to a coiled conformation at low pH.
Co-reporter:Sudipta Majumdar, Agnes Hajduczki, Aaron S. Mendez, Gregory A. Weiss
Bioorganic & Medicinal Chemistry Letters 2008 Volume 18(Issue 22) pp:5937-5940
Publication Date(Web):15 November 2008
DOI:10.1016/j.bmcl.2008.07.051
Phage display of protein and peptide libraries offers a powerful technology for the selection and isolation of ligands and receptors. To date, the technique has been considered limited to soluble, non-membrane proteins. We report two examples of phage display of full-length, folded and functional membrane proteins. Consistent display required the recently reported KO7+ helper phage. The two proteins, full-length caveolin-1 and HIV gp41, display well on the surface of the phage, and maintain their binding activities as shown by in vitro assays.
Co-reporter:Jorge A. Lamboy;Phillip Y. Tam Dr.;Lucie S. Lee;Pilgrim J. Jackson Dr.;Sara K. Avrantinis Dr.;Hye J. Lee ;Robert M. Corn
ChemBioChem 2008 Volume 9( Issue 17) pp:2846-2852
Publication Date(Web):
DOI:10.1002/cbic.200800366
Abstract
An Achilles heel inherent to all molecular display formats, background binding between target and display system introduces false positives into screens and selections. For example, the negatively charged surfaces of phage, mRNA, and ribosome display systems bind with unacceptably high nonspecificity to positively charged target molecules, which represent an estimated 35 % of proteins in the human proteome. Here we report the first systematic attempt to understand why a broad class of molecular display selections fail, and then solve the underlying problem for both phage and RNA display. Firstly, a genetic strategy was used to introduce a short, charge-neutralizing peptide into the solvent-exposed, negatively charged phage coat. The modified phage (KO7+) reduced or eliminated nonspecific binding to the problematic high-pI proteins. In the second, chemical approach, nonspecific interactions were blocked by oligolysine wrappers in the cases of phage and total RNA. For phage display applications, the peptides Lysn (where n=16 to 24) emerged as optimal for wrapping the phage. Lys8, however, provided effective wrappers for RNA binding in assays against the RNA binding protein HIV-1 Vif. The oligolysine peptides blocked nonspecific binding to allow successful selections, screens, and assays with five previously unworkable protein targets.
Co-reporter:Jorge A. Lamboy;Phillip Y. Tam Dr.;Lucie S. Lee;Pilgrim J. Jackson Dr.;Sara K. Avrantinis Dr.;Hye J. Lee ;Robert M. Corn
ChemBioChem 2008 Volume 9( Issue 17) pp:
Publication Date(Web):
DOI:10.1002/cbic.200890066
Co-reporter:Aron M. Levin, Katsuyuki Murase, Pilgrim J. Jackson, Mack L. Flinspach, Thomas L. Poulos and Gregory A. Weiss
ACS Chemical Biology 2007 Volume 2(Issue 7) pp:493
Publication Date(Web):June 29, 2007
DOI:10.1021/cb700055t
In the postgenomic era, a major challenge remains, elucidating the thermodynamic forces governing receptor–ligand specificity and promiscuity. We report a straightforward approach for mapping side-chain contributions to binding for the multipartner interactions characteristic of the human proteome. Double barrel shotgun scanning dissects binding to two or more targets through combinatorial mutagenesis of one protein binding to multiple targets. Examined here, the caveolin-1 scaffolding domain (CSD) binds to and inhibits both endothelial nitric oxide synthase (eNOS) and protein kinase A (PKA). Homolog shotgun scanning of CSD highlights residues responsible for CSD oligomerization and binding to eNOS and PKA. The experiments uncover a general mechanism in which CSD oligomerizes and deoligomerizes to modulate binding affinity to partner proteins. The results provide a detailed look at a multipartner protein interaction, uncovering strategies for one protein binding to multiple partners.
Co-reporter:A. M. Levin and G. A. Weiss
Molecular BioSystems 2006 vol. 2(Issue 1) pp:49-57
Publication Date(Web):08 Nov 2005
DOI:10.1039/B511782H
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.
Co-reporter:Allison Olszewski;Zachary D. Aron;Frederick Cohen;Ken Sato;Aleishia Harris;Brenda R. McDougall;Larry E. Overman;W. Edward Robinson, Jr.
PNAS 2004 Volume 101 (Issue 39 ) pp:14079-14084
Publication Date(Web):2004-09-28
DOI:10.1073/pnas.0406040101
With current anti-HIV treatments targeting only 4 of the 15 HIV proteins, many potential viral vulnerabilities remain unexploited.
We report small-molecule inhibitors of the HIV-1 protein Nef. In addition to expanding the anti-HIV arsenal, small-molecule
inhibitors against untargeted HIV proteins could be used to dissect key events in the HIV lifecycle. Numerous incompletely
characterized interactions between Nef and cellular ligands, for example, present a challenge to understanding molecular events
during HIV progression to AIDS. Assays with phage-displayed Nef from HIVNL4-3 were used to identify a series of guanidine alkaloid-based inhibitors of Nef interactions with p53, actin, and p56lck. The guanidines, synthetic analogs of batzellidine and crambescidin natural products, inhibit the Nef–ligand interactions
with IC50 values in the low micromolar range. In addition, sensitive in vivo assays for Nef inhibition are reported. Although compounds that are effective in vitro proved to be too cytotoxic for cellular assays, the reported Nef inhibitors provide proof-of-concept for disrupting a new
HIV target and offer useful leads for drug development.
Co-reporter:Sara K. Avrantinis;Ryan L. Stafford;Xia Tian
ChemBioChem 2002 Volume 3(Issue 12) pp:
Publication Date(Web):3 DEC 2002
DOI:10.1002/1439-7633(20021202)3:12<1229::AID-CBIC1229>3.0.CO;2-X
Shotgun scanning the streptavidin–biotin interaction identifies long-range hydrophobic interactions that contribute to one of the strongest naturally occurring noncovalent protein–ligand interactions. The femtomolar dissociation constant for this interaction makes it a useful model system to dissect the forces that govern high-affinity molecular recognition between proteins and small molecules. Shotgun scanning combines the diversity and in vitro binding selection of phage-displayed libraries with a binomial mutagenesis strategy. Libraries consist of proteins with the residues in multiple positions mutated to give a 1:1 ratio of alanine:wild type. Here, we use shotgun scanning to determine the functional contribution of the 38 C-terminal residues of streptavidin to the high-affinity interaction with biotin. The library pools were subjected to three rounds of selection for functional streptavidin variants that bind biotin and statistical analysis was used to assess side-chain contributions to biotin binding. The results demonstrate the utility of shotgun scanning for the dissection of receptor–small-molecule interactions. While shotgun scanning results were largely consistent with previous single-point, site-directed mutagenesis studies for residues in direct contact with biotin, residues distant from the biotin binding site have not previously been explored. Key streptavidin residues identified by shotgun scanning as contributors to the interaction with biotin include those with side chains that fill the β barrel, residues at the tetramer interface, and second-sphere residues, which are reinforced by long-distance propagation of hydrophobic interactions.
Co-reporter:Rosemarie Vithayathil, Richard M. Hooy, Melanie J. Cocco, Gregory A. Weiss
Journal of Molecular Biology (9 December 2011) Volume 414(Issue 4) pp:499-510
Publication Date(Web):9 December 2011
DOI:10.1016/j.jmb.2011.10.021
Numerous examples of phage display applied to soluble proteins demonstrate the power of the technique for protein engineering, affinity reagent discovery and structure–function studies. Recent reports have expanded phage display to include membrane proteins (MPs). The scope and limitations of MP display remain undefined. Therefore, we report data from the phage display of representative types of membrane-associated proteins including plasma, nuclear, peripheral, single and multipass. The peripheral MP neuromodulin displays robustly with packaging by conventional M13-KO7 helper phage. The monotopic MP Nogo-66 can also display on the phage surface, if packaged by the modified M13-KO7+ helper phage. The modified phage coat of KO7+ can better mimic the zwitterionic character of the plasma membrane. Four examples of putatively α-helical, integral MPs failed to express as fusions to an anchoring phage coat protein and therefore did not display on the phage surface. However, the β-barrel MPs ShuA (Shigella heme uptake A) and MOMP (major outer membrane protein), which pass through the membrane 22 and 16 times, respectively, can display surprisingly well on the surfaces of both conventional and KO7+ phages. The results provide a guide for protein engineering and large-scale mutagenesis enabled by the phage display of MPs.Download high-res image (179KB)Download full-size imageResearch Highlights► Phage display works well for some, but not all, MPs. ► KO7+ helper phage allows display of Nogo-66 and caveolin-1 monotopic MPs. ► Multipass α-helical MPs fail to display in several attempts. ► Unexpectedly, β-barrel MPs display well on both conventional and KO7+ surfaces.
Co-reporter:Joshua Britton, Colin L. Raston and Gregory A. Weiss
Chemical Communications 2016 - vol. 52(Issue 66) pp:NaN10162-10162
Publication Date(Web):2016/07/19
DOI:10.1039/C6CC04210D
A versatile enzyme immobilization strategy for thin film continuous flow processing is reported. Here, non-covalent and glutaraldehyde bioconjugation are used to immobilize enzymes on the surfaces of borosilicate reactors. This approach requires only ng of protein per reactor tube, with the stock protein solution readily recycled to sequentially coat >10 reactors. Confining reagents to thin films during immobilization reduced the amount of protein, piranha-cleaning solution, and other reagents by ∼96%. Through this technique, there was no loss of catalytic activity over 10 h processing. The results reported here combines the benefits of thin film flow processing with the mild conditions of biocatalysis.