1
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Boissieras J, Bonnet H, Susanto MF, Gomez D, Defrancq E, Granzhan A, Dejeu J. iMab antibody binds single-stranded cytosine-rich sequences and unfolds DNA i-motifs. Nucleic Acids Res 2024; 52:8052-8062. [PMID: 38908025 DOI: 10.1093/nar/gkae531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024] Open
Abstract
i-Motifs (iMs) are non-canonical, four-stranded secondary structures formed by stacking of hemi-protonated CH+·C base pairs in cytosine-rich DNA sequences, predominantly at pH < 7. The presence of iM structures in cells was a matter of debate until the recent development of iM-specific antibody, iMab, which was instrumental for several studies that suggested the existence of iMs in live cells and their putative biological roles. We assessed the interaction of iMab with cytosine-rich oligonucleotides by biolayer interferometry (BLI), pull-down assay and bulk-FRET experiments. Our results suggest that binding of iMab to DNA oligonucleotides is governed by the presence of runs of at least two consecutive cytosines and is generally increased in acidic conditions, irrespectively of the capacity of the sequence to adopt, or not, an iM structure. Moreover, the results of the bulk-FRET assay indicate that interaction with iMab results in unfolding of iM structures even in acidic conditions, similarly to what has been observed with hnRNP K, well-studied single-stranded DNA binding protein. Taken together, our results strongly suggest that iMab actually binds to blocks of 2-3 cytosines in single-stranded DNA, and call for more careful interpretation of results obtained with this antibody.
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Affiliation(s)
- Joseph Boissieras
- Chemistry and Modelling for Biology of Cancer (CMBC), CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405 Orsay, France
| | - Hugues Bonnet
- Département de Chimie Moléculaire (DCM), CNRS UMR5250, Université Grenoble-Alpes, 38000 Grenoble, France
| | - Maria Fidelia Susanto
- Institut de Pharmacologie et Biologie Structurale (IPBS), CNRS UMR5089, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Dennis Gomez
- Institut de Pharmacologie et Biologie Structurale (IPBS), CNRS UMR5089, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Eric Defrancq
- Département de Chimie Moléculaire (DCM), CNRS UMR5250, Université Grenoble-Alpes, 38000 Grenoble, France
| | - Anton Granzhan
- Chemistry and Modelling for Biology of Cancer (CMBC), CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405 Orsay, France
| | - Jérôme Dejeu
- Département de Chimie Moléculaire (DCM), CNRS UMR5250, Université Grenoble-Alpes, 38000 Grenoble, France
- SUPMICROTECH, Université Franche-Comté, Institut FEMTO-ST, 25000 Besançon, France
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2
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Kojima T, Nakane A, Zhu B, Alfi A, Nakano H. A simple, real-time assay of horseradish peroxidase using biolayer interferometry. Biosci Biotechnol Biochem 2019; 83:1822-1828. [PMID: 31119970 DOI: 10.1080/09168451.2019.1621156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Horseradish peroxidase (HRP) isoenzyme C1a is one of the most widely used enzymes for various analytical methods in bioscience research and medical fields. In these fields, real-time monitoring of HRP activity is highly desirable because the utility of HRP as a reporter enzyme would be expanded. In this study, we developed a simple assay system enabling real-time monitoring of HRP activity by using biolayer interferometry (BLI). The HRP activity was quantitatively detected on a BLI sensor chip by tracing a binding response of tyramide, a substrate of HRP, onto an immobilized protein. This system could be applied to analyses related to oxidase activity, as well as to the functional analysis of recombinant HRP.
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Affiliation(s)
- Takaaki Kojima
- Graduate School of Bioagricultural Sciences, Nagoya University , Chikusa-ku, Nagoya , Japan
| | - Ayako Nakane
- Graduate School of Bioagricultural Sciences, Nagoya University , Chikusa-ku, Nagoya , Japan
| | - Bo Zhu
- Graduate School of Bioagricultural Sciences, Nagoya University , Chikusa-ku, Nagoya , Japan
| | - Almasul Alfi
- Graduate School of Bioagricultural Sciences, Nagoya University , Chikusa-ku, Nagoya , Japan
| | - Hideo Nakano
- Graduate School of Bioagricultural Sciences, Nagoya University , Chikusa-ku, Nagoya , Japan
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3
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Machen AJ, O'Neil PT, Pentelute BL, Villar MT, Artigues A, Fisher MT. Analyzing Dynamic Protein Complexes Assembled On and Released From Biolayer Interferometry Biosensor Using Mass Spectrometry and Electron Microscopy. J Vis Exp 2018. [PMID: 30124667 PMCID: PMC6126661 DOI: 10.3791/57902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In vivo, proteins are often part of large macromolecular complexes where binding specificity and dynamics ultimately dictate functional outputs. In this work, the pre-endosomal anthrax toxin is assembled and transitioned into the endosomal complex. First, the N-terminal domain of a cysteine mutant lethal factor (LFN) is attached to a biolayer interferometry (BLI) biosensor through disulfide coupling in an optimal orientation, allowing protective antigen (PA) prepore to bind (Kd 1 nM). The optimally oriented LFN-PAprepore complex then binds to soluble capillary morphogenic gene-2 (CMG2) cell surface receptor (Kd 170 pM), resulting in a representative anthrax pre-endosomal complex, stable at pH 7.5. This assembled complex is then subjected to acidification (pH 5.0) representative of the late endosome environment to transition the PAprepore into the membrane inserted pore state. This PApore state results in a weakened binding between the CMG2 receptor and the LFN-PApore and a substantial dissociation of CMG2 from the transition pore. The thio-attachment of LFN to the biosensor surface is easily reversed by dithiothreitol. Reduction on the BLI biosensor surface releases the LFN-PAprepore-CMG2 ternary complex or the acid transitioned LFN-PApore complexes into microliter volumes. Released complexes are then visualized and identified using electron microscopy and mass spectrometry. These experiments demonstrate how to monitor the kinetic assembly/disassembly of specific protein complexes using label-free BLI methodologies and evaluate the structure and identity of these BLI assembled complexes by electron microscopy and mass spectrometry, respectively, using easy-to-replicate sequential procedures.
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Affiliation(s)
- Alexandra J Machen
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center
| | - Pierce T O'Neil
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center
| | | | - Maria T Villar
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center
| | - Antonio Artigues
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center
| | - Mark T Fisher
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center;
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4
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O'Neil PT, Machen AJ, Deatherage BC, Trecazzi C, Tischer A, Machha VR, Auton MT, Baldwin MR, White TA, Fisher MT. The Chaperonin GroEL: A Versatile Tool for Applied Biotechnology Platforms. Front Mol Biosci 2018; 5:46. [PMID: 29868607 PMCID: PMC5962814 DOI: 10.3389/fmolb.2018.00046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/23/2018] [Indexed: 01/06/2023] Open
Abstract
The nucleotide-free chaperonin GroEL is capable of capturing transient unfolded or partially unfolded states that flicker in and out of existence due to large-scale protein dynamic vibrational modes. In this work, three short vignettes are presented to highlight our continuing advances in the application of GroEL biosensor biolayer interferometry (BLI) technologies and includes expanded uses of GroEL as a molecular scaffold for electron microscopy determination. The first example presents an extension of the ability to detect dynamic pre-aggregate transients in therapeutic protein solutions where the assessment of the kinetic stability of any folded protein or, as shown herein, quantitative detection of mutant-type protein when mixed with wild-type native counterparts. Secondly, using a BLI denaturation pulse assay with GroEL, the comparison of kinetically controlled denaturation isotherms of various von Willebrand factor (vWF) triple A domain mutant-types is shown. These mutant-types are single point mutations that locally disorder the A1 platelet binding domain resulting in one gain of function and one loss of function phenotype. Clear, separate, and reproducible kinetic deviations in the mutant-type isotherms exist when compared with the wild-type curve. Finally, expanding on previous electron microscopy (EM) advances using GroEL as both a protein scaffold surface and a release platform, examples are presented where GroEL-protein complexes can be imaged using electron microscopy tilt series and the low-resolution structures of aggregation-prone proteins that have interacted with GroEL. The ability of GroEL to bind hydrophobic regions and transient partially folded states allows one to employ this unique molecular chaperone both as a versatile structural scaffold and as a sensor of a protein's folded states.
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Affiliation(s)
- Pierce T O'Neil
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Alexandra J Machen
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Benjamin C Deatherage
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Caleb Trecazzi
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Alexander Tischer
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Venkata R Machha
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Matthew T Auton
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Michael R Baldwin
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
| | - Tommi A White
- Department of Biochemistry, University of Missouri, Columbia, MO, United States.,Electron Microscopy Core Facility, University of Missouri, Columbia, MO, United States
| | - Mark T Fisher
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States
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5
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Pace SE, Joshi SB, Esfandiary R, Stadelman R, Bishop SM, Middaugh CR, Fisher MT, Volkin DB. The Use of a GroEL-BLI Biosensor to Rapidly Assess Preaggregate Populations for Antibody Solutions Exhibiting Different Stability Profiles. J Pharm Sci 2017; 107:559-570. [PMID: 29037466 DOI: 10.1016/j.xphs.2017.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/02/2017] [Accepted: 10/05/2017] [Indexed: 11/29/2022]
Abstract
An automated method using biotinylated GroEL-streptavidin biosensors with biolayer interferometry (GroEL-BLI) was evaluated to detect the formation of transiently formed, preaggregate species in various pharmaceutically relevant monoclonal antibody (mAb) samples. The relative aggregation propensity of various IgG1 and IgG4 mAbs was rank ordered using the GroEL-BLI biosensor method, and the least stable IgG4 mAb was subjected to different stresses including elevated temperatures, acidic pH, and addition of guanidine HCl. The GroEL-BLI biosensor detects mAb preaggregate formation mostly before, or sometimes concomitantly with, observing soluble aggregates and subvisible particles using size-exclusion chromatography and microflow imaging, respectively. A relatively unstable bispecific antibody (Bis-3) was shown to bind the GroEL biosensor even at low temperatures (25°C). During thermal stress (50°C, 1 h), increased Bis-3 binding to GroEL-biosensors was observed prior to aggregation by size-exclusion chromatography or microflow imaging. Transmission electron microscopy analysis of Bis-3 preaggregate GroEL complexes revealed, in some cases, potential hydrophobic interaction sites between the Fc domain of the Bis-3 and GroEL protein. The automated BLI method not only enables detection of transiently formed preaggregate species that initiate protein aggregation pathways but also permits rapid mAb formulation stability assessments at low volumes and low protein concentrations.
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Affiliation(s)
- Samantha E Pace
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047
| | - Sangeeta B Joshi
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047
| | - Reza Esfandiary
- Department of Formulation Sciences, MedImmune, One MedImmune Way, Gaithersburg, Maryland 20878
| | - Robert Stadelman
- Department of Cell Culture and Fermentation Sciences, MedImmune, One MedImmune Way, Gaithersburg, Maryland 20878
| | - Steven M Bishop
- Department of Formulation Sciences, MedImmune, One MedImmune Way, Gaithersburg, Maryland 20878
| | - C R Middaugh
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047
| | - Mark T Fisher
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160.
| | - David B Volkin
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047.
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6
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Zhao B, Zhang Y, Huang Y, Yu J, Li Y, Wang Q, Ma Y, Song HY, Yu M, Mo W. A novel hirudin derivative inhibiting thrombin without bleeding for subcutaneous injection. Thromb Haemost 2016; 117:44-56. [PMID: 27904902 DOI: 10.1160/th16-05-0416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 09/17/2016] [Indexed: 12/29/2022]
Abstract
Currently, anticoagulants would be used to prevent thrombosis. Thrombin is an effector enzyme for haemostasis and thrombosis. We designed a direct thrombin inhibitor peptide (DTIP) using molecular simulation and homology modelling and demonstrated that the C-terminus of DTIP interacts with exosite I, and N-terminus with the activity site of thrombin, respectively. DTIP interfered with thrombin-mediated coagulation in human, rat and mouse plasma (n=10 per group) and blocked clotting in human whole blood in vitro. When administered subcutaneously, DTIP showed potent and dose-dependent extension of aPTT, PT, TT and CT in rats (n=10 per group). The antithrombotic dose of DTIP induced significantly less bleeding than bivalirudin determined by transecting distal tail assay in rats. Furthermore, DTIP reached peak blood concentration in 0.5-1 hour and did not cause increased bleeding after five days of dosing compared to dabigatran etexilate. The antithrombotic effect of DTIP was evaluated in mice using lethal pulmonary thromboembolism model and FeCl3-induced mesenteric arteriole thrombus model. DTIP (1.0 mg/kg, sc) prevented deep venous thrombosis and increased the survival rate associated with pulmonary thromboembolism from 30 % to 80 %. Intravital microscopy showed that DTIP (1.0 mg/kg, sc) decelerated mesenteric arteriole thrombosis caused by FeCl3 injury. These data establish that DTIP is a novel antithrombotic agent that could be used to prevent thrombosis without conferring an increased bleeding risk.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Wei Mo
- Wei Mo, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University, Tel.: +86 21 54237440, Fax: +86 21 64033738, 238# P.O. Box, 138 Yixueyan Rd., Shanghai, 200032 , P. R. China, E-mail:
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7
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Lea WA, O'Neil PT, Machen AJ, Naik S, Chaudhri T, McGinn-Straub W, Tischer A, Auton MT, Burns JR, Baldwin MR, Khar KR, Karanicolas J, Fisher MT. Chaperonin-Based Biolayer Interferometry To Assess the Kinetic Stability of Metastable, Aggregation-Prone Proteins. Biochemistry 2016; 55:4885-908. [PMID: 27505032 DOI: 10.1021/acs.biochem.6b00293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Stabilizing the folded state of metastable and/or aggregation-prone proteins through exogenous ligand binding is an appealing strategy for decreasing disease pathologies caused by protein folding defects or deleterious kinetic transitions. Current methods of examining binding of a ligand to these marginally stable native states are limited because protein aggregation typically interferes with analysis. Here, we describe a rapid method for assessing the kinetic stability of folded proteins and monitoring the effects of ligand stabilization for both intrinsically stable proteins (monomers, oligomers, and multidomain proteins) and metastable proteins (e.g., low Tm) that uses a new GroEL chaperonin-based biolayer interferometry (BLI) denaturant pulse platform. A kinetically controlled denaturation isotherm is generated by exposing a target protein, immobilized on a BLI biosensor, to increasing denaturant concentrations (urea or GuHCl) in a pulsatile manner to induce partial or complete unfolding of the attached protein population. Following the rapid removal of the denaturant, the extent of hydrophobic unfolded/partially folded species that remains is detected by an increased level of GroEL binding. Because this kinetic denaturant pulse is brief, the amplitude of binding of GroEL to the immobilized protein depends on the duration of the exposure to the denaturant, the concentration of the denaturant, wash times, and the underlying protein unfolding-refolding kinetics; fixing all other parameters and plotting the GroEL binding amplitude versus denaturant pulse concentration result in a kinetically controlled denaturation isotherm. When folding osmolytes or stabilizing ligands are added to the immobilized target proteins before and during the denaturant pulse, the diminished population of unfolded/partially folded protein manifests as a decreased level of GroEL binding and/or a marked shift in these kinetically controlled denaturation profiles to higher denaturant concentrations. This particular platform approach can be used to identify small molecules and/or solution conditions that can stabilize or destabilize thermally stable proteins, multidomain proteins, oligomeric proteins, and, most importantly, aggregation-prone metastable proteins.
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Affiliation(s)
- Wendy A Lea
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Pierce T O'Neil
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Alexandra J Machen
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | - Subhashchandra Naik
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
| | | | - Wesley McGinn-Straub
- fortéBIO (a division of Pall Life Sciences) , Menlo Park, California 94025, United States
| | - Alexander Tischer
- Division of Hematology, Department of Internal Medicine, Mayo Clinic , Rochester, Minnesota 55902, United States
| | - Matthew T Auton
- Division of Hematology, Department of Internal Medicine, Mayo Clinic , Rochester, Minnesota 55902, United States
| | - Joshua R Burns
- Department of Molecular Microbiology and Immunology, University of Missouri , Columbia, Missouri 65212, United States
| | - Michael R Baldwin
- Department of Molecular Microbiology and Immunology, University of Missouri , Columbia, Missouri 65212, United States
| | - Karen R Khar
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
| | - John Karanicolas
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
| | - Mark T Fisher
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States
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8
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Pastor A, Singh AK, Fisher MT, Chaudhuri TK. Protein folding on biosensor tips: folding of maltodextrin glucosidase monitored by its interactions with GroEL. FEBS J 2016; 283:3103-14. [PMID: 27367928 DOI: 10.1111/febs.13796] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/29/2016] [Accepted: 06/29/2016] [Indexed: 01/16/2023]
Abstract
Protein folding has been extensively studied for the past six decades by employing solution-based methods such as solubility, enzymatic activity, secondary structure analysis, and analytical methods like FRET, NMR, and HD exchange. However, for rapid analysis of the folding process, solution-based approaches are often plagued with aggregation side reactions resulting in poor yields. In this work, we demonstrate that a bio-layer interferometry (BLI) chaperonin detection system can identify superior refolding conditions for denatured proteins. The degree of immobilized protein folding as a function of time can be detected by monitoring the binding of the high-affinity nucleotide-free form of the chaperonin GroEL. GroEL preferentially interacts with proteins that have hydrophobic surfaces exposed in their unfolded or partially folded form, so a decrease in GroEL binding can be correlated with burial of hydrophobic surfaces as folding progresses. The magnitude of GroEL binding to the protein immobilized on bio-layer interferometry biosensor inversely reflects the extent of protein folding and hydrophobic residue burial. We demonstrate conditions where accelerated folding can be observed for the aggregation-prone protein maltodextrin glucosidase (MalZ). Superior immobilized folding conditions identified on the bio-layer interferometry biosensor surface were reproduced on Ni-NTA sepharose bead surfaces and resulted in significant improvement in folding yields of released MalZ (measured by enzymatic activity) compared to bulk refolding conditions in solution.
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Affiliation(s)
- Ashutosh Pastor
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
| | - Amit K Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
| | - Mark T Fisher
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Centre, KS, USA
| | - Tapan K Chaudhuri
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
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9
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Chan CP. Forced degradation studies: current trends and future perspectives for protein-based therapeutics. Expert Rev Proteomics 2016; 13:651-8. [DOI: 10.1080/14789450.2016.1200469] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Christine P. Chan
- Global Manufacturing Science & Technology, Specialty Care Operations, Sanofi, Framingham, MA, USA
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10
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Akkaladevi N, Mukherjee S, Katayama H, Janowiak B, Patel D, Gogol EP, Pentelute BL, Collier RJ, Fisher MT. Following Natures Lead: On the Construction of Membrane-Inserted Toxins in Lipid Bilayer Nanodiscs. J Membr Biol 2015; 248:595-607. [PMID: 25578459 PMCID: PMC4580227 DOI: 10.1007/s00232-014-9768-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/22/2014] [Indexed: 11/27/2022]
Abstract
Bacterial toxin or viral entry into the cell often requires cell surface binding and endocytosis. The endosomal acidification induces a limited unfolding/refolding and membrane insertion reaction of the soluble toxins or viral proteins into their translocation competent or membrane inserted states. At the molecular level, the specific orientation and immobilization of the pre-transitioned toxin on the cell surface is often an important prerequisite prior to cell entry. We propose that structures of some toxin membrane insertion complexes may be observed through procedures where one rationally immobilizes the soluble toxin so that potential unfolding ↔ refolding transitions that occur prior to membrane insertion orientate away from the immobilization surface in the presence of lipid micelle pre-nanodisc structures. As a specific example, the immobilized prepore form of the anthrax toxin pore translocon or protective antigen can be transitioned, inserted into a model lipid membrane (nanodiscs), and released from the immobilized support in its membrane solubilized form. This particular strategy, although unconventional, is a useful procedure for generating pure membrane-inserted toxins in nanodiscs for electron microscopy structural analysis. In addition, generating a similar immobilized platform on label-free biosensor surfaces allows one to observe the kinetics of these acid-induced membrane insertion transitions. These platforms can facilitate the rational design of inhibitors that specifically target the toxin membrane insertion transitions that occur during endosomal acidification. This approach may lead to a new class of direct anti-toxin inhibitors.
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Affiliation(s)
- Narahari Akkaladevi
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Srayanta Mukherjee
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Hiroo Katayama
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Blythe Janowiak
- Department of Biology, Saint Louis University, St. Louis, MO 63101, USA
| | - Deepa Patel
- Department of Microbiology and Molecular Genetics, Harvard University, Boston, MA, USA
| | - Edward P. Gogol
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02193, USA
| | - R. John Collier
- Department of Microbiology and Molecular Genetics, Harvard University, Boston, MA, USA
| | - Mark T. Fisher
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
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11
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Yu T, Gao X, Ren Y, Wei D. Assembly of cellulases with synthetic protein scaffolds in vitro. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-015-0046-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Abstract
Background
Enzymatic cascades in metabolic pathways are spatially organized in such a way as to facilitate the flow of substrates. The construction of artificial cellulase complexes that mimic natural multienzyme assemblies can potentially enhance the capacity for cellulose hydrolysis. In this study, an artificial cellulase complex was constructed by tethering three cellulases to a synthetic protein scaffold.
Results
Three pairs of interacting proteins were selected and characterized. The artificial protein scaffolds were constructed by fusing three interacting proteins. Cellulases were tethered to these synthetic scaffolds in different orders. The optimal assembly resulted in a 1.5-fold higher hydrolysis of cellulose than that achieved by unassembled cellulases.
Conclusions
A novel artificial protein scaffold was constructed and used to assemble three cellulases. The resultant increase in enzymatic activity suggests that this can be used as a strategy for enhancing the biocatalytic capacity of enzyme cascades.
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12
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Majumdar R, Middaugh C, Weis DD, Volkin DB. Hydrogen-Deuterium Exchange Mass Spectrometry as an Emerging Analytical Tool for Stabilization and Formulation Development of Therapeutic Monoclonal Antibodies. J Pharm Sci 2015; 104:327-45. [DOI: 10.1002/jps.24224] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 12/11/2022]
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13
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Davis MI, Simeonov A, Lea W, Auld D. Literature Search and Review. Assay Drug Dev Technol 2015. [DOI: 10.1089/adt.2014.1210.lr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | | | - Doug Auld
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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14
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Correia AR, Naik S, Fisher MT, Gomes CM. Probing the kinetic stabilities of Friedreich's ataxia clinical variants using a solid phase GroEL chaperonin capture platform. Biomolecules 2014; 4:956-79. [PMID: 25333765 PMCID: PMC4279165 DOI: 10.3390/biom4040956] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 08/29/2014] [Accepted: 09/19/2014] [Indexed: 11/17/2022] Open
Abstract
Numerous human diseases are caused by protein folding defects where the protein may become more susceptible to degradation or aggregation. Aberrant protein folding can affect the kinetic stability of the proteins even if these proteins appear to be soluble in vivo. Experimental discrimination between functional properly folded and misfolded nonfunctional conformers is not always straightforward at near physiological conditions. The differences in the kinetic behavior of two initially folded frataxin clinical variants were examined using a high affinity chaperonin kinetic trap approach at 25 °C. The kinetically stable wild type frataxin (FXN) shows no visible partitioning onto the chaperonin. In contrast, the clinical variants FXN-p.Asp122Tyr and FXN-p.Ile154Phe kinetically populate partial folded forms that tightly bind the GroEL chaperonin platform. The initially soluble FXN-p.Ile154Phe variant partitions onto GroEL more rapidly and is more kinetically liable. These differences in kinetic stability were confirmed using differential scanning fluorimetry. The kinetic and aggregation stability differences of these variants may lead to the distinct functional impairments described in Friedreich's ataxia, the neurodegenerative disease associated to frataxin functional deficiency. This chaperonin platform approach may be useful for identifying small molecule stabilizers since stabilizing ligands to frataxin variants should lead to a concomitant decrease in chaperonin binding.
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Affiliation(s)
- Ana R Correia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, Oeiras 2784-505, Portugal.
| | - Subhashchandra Naik
- Department of Biochemistry and Molecular Biology, Hemenway Life Sciences Innovation Center (HLSIC), University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA.
| | - Mark T Fisher
- Department of Biochemistry and Molecular Biology, Hemenway Life Sciences Innovation Center (HLSIC), University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA.
| | - Cláudio M Gomes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, Oeiras 2784-505, Portugal.
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