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Hosseini E, Taherabadi E, Rajabi A, Ghasemzadeh M. Reduction of ristocetin-induced platelet aggregation (RIPA) during storage despite plasma renewal: evidence for hemostatic importance of GPIbα shedding. Expert Rev Hematol 2024; 17:391-403. [PMID: 38889268 DOI: 10.1080/17474086.2024.2370557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/25/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Platelet storage is complicated by deleterious changes, among which reduction of ristocetin-induced platelet aggregation (RIPA) has a poorly understood mechanism. The study elucidates the mechanistic roles of all the possible players in this process. RESEARCH DESIGN AND METHODS PRP-platelet concentrates were subjected to RIPA, collagen-induced platelet aggregation (CIPA), and flowcytometric analysis of GPIbα and PAC-1 binding from days 0 to 5 of storage. Platelet-poor plasma was subjected to colorimetric assays for glucose/LDH evaluation and automatic analyzer to examine VWF antigen and activity. RESULTS From day three of platelet storage, reducing CIPA but not RIPA was correlated with the reduction of both metabolic state and integrin activity. RIPA reduction was directly related to the decreased levels of total-content/expression of GPIbα, and inversely related to its shedding levels during storage. Re-suspension of 5-day stored platelet in fresh plasma compensated CIPA, but not RIPA. VWF concentration and its activity did not change during storage while they had no correlation with RIPA. CONCLUSIONS This study identified the irreversible loss of platelet GPIbα, but not VWF status, as the primary cause of the storage-dependent decrease of RIPA. Unlike CIPA, this observation was not compensated by plasma refreshment, suggesting that some evidence of PSL may not be recovered after transfusion.
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Affiliation(s)
- Ehteramolsadat Hosseini
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Emad Taherabadi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Ali Rajabi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Mehran Ghasemzadeh
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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Pawaskar GM, Raval R. Development of a fluorescence-based excipient screening for improved stability and shelf-life of recombinant chitin deacetylase. Biochem Biophys Rep 2024; 38:101718. [PMID: 38708424 PMCID: PMC11066597 DOI: 10.1016/j.bbrep.2024.101718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/19/2024] [Indexed: 05/07/2024] Open
Abstract
Chitin deacetylase (CDA) modifies chitin into chitosan by removing acetyl groups, but its inherent instability poses a challenge for successful crystallisation. Despite limited successes in crystallizing CDAs, prior attempts with recombinant chitin deacetylase (BaCDA) failed due to poor stability. To address this, we propose an enzyme buffer formulation as a cost-effective strategy to enhance stability, prolong shelf life, and increase the likelihood of crystallisation. Utilizing the high-throughput screening technique FTSA, we developed a screening method correlating BaCDA stability with its activity. The optimised formulation comprises 50 mM Tris-HCl buffer pH 7, 1 M NaCl, 20 % glycerol, and 1 mM Mg2+ as excipients. This formulation significantly improves BaCDA's thermostability (140.47 % increase) and enzyme activity (2.9-fold enhancement). BaCDA remains stable in the formulated buffer at -20 °C and -80 °C for 30 days and at 4 °C for 15 days. The current study has designed a high-throughput screening method approach to assess the stability of CDA enzyme formulations. The results of this study could contribute to the exploration of formulation elements that enhance the structural stability of CDA, thereby facilitating investigations into the enzyme's structure-function relationships.
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Affiliation(s)
- Goutam Mohan Pawaskar
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Ritu Raval
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
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Wan Nazri WSM, Ling LY, Wen CF. Detection of Plasmodium knowlesi in whole blood samples with sandwich enzyme-linked immunosorbent assay (ELISA) using rhoptry-associated protein 1 specific polyclonal antibodies. J Vector Borne Dis 2024; 61:203-210. [PMID: 38922654 DOI: 10.4103/jvbd.jvbd_55_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/06/2023] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND OBJECTIVES Plasmodium knowlesi, a simian malaria species, is now known to infect humans. Due to disadvantages in the current diagnosis methods, many efforts have been placed into developing new methods to diagnose the disease. This study assessed the ability of the PkRAP-1 sandwich enzyme-linked immunosorbent (ELISA) to detect P knowlesi antigens in whole blood specimens. METHODS Western blot assay was conducted to evaluate the ability of raised mouse and rabbit anti-PkRAP-1 polyclonal antibodies to bind to the native proteins in P. knowlesi lysate. The polyclonal antibodies were then used in sandwich ELISA to detect P. knowlesi. In the sandwich ELISA, mouse and rabbit polyclonal antibodies were used as the capture and detection antibodies, respectively. The limit of detection (LOD) of the assay was determined using P. knowlesi A1H1 culture and purified recombinant PkRAP-1. RESULTS Western blot results showed positive reactions towards the proteins in P. knowlesi lysate. The LOD of the assay from three technical replicates was 0.068% parasitaemia. The assay performance in detecting P. knowlesi was 83% sensitivity and 70% specificity with positive and negative predictive values of 74% and 80%, respectively. The anti-PkRAP-1 polyclonal antibodies did not cross-react with P. falciparum and healthy samples, but P. vivax by detecting all 12 samples. INTERPRETATION CONCLUSION PkRAP-1 has the potential as a biomarker for the development of a new diagnostic tool for P. knowlesi detection. Further studies need to be conducted to establish the full potential of the usage of anti-PkRAP-1 antibodies for P. knowlesi detection.
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Kamrani S, Yaghmaei P, Nikkhah M, Hosseinkhani S. Spectroscopic analysis of recombinant human growth hormone in the presence of sucrose and trehalose. Biotechnol Appl Biochem 2023; 70:1543-1553. [PMID: 36807340 DOI: 10.1002/bab.2452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/11/2023] [Indexed: 02/19/2023]
Abstract
Recombinant human growth hormone (rhGH) is a therapeutic protein, associated with various human diseases, such as growth hormone deficiency. One of the interesting issues in the formulation of therapeutic proteins is excipients like disaccharides. In the current study, we try to compare the effect of sucrose and trehalose on the structure of rhGH in the liquid state at 25°C and 55°C. We use spectroscopic techniques including intrinsic and extrinsic fluorescence, Fourier-transform infrared (FTIR), circular dichroism (CD), dynamic light scattering (DLS), and time-resolved fluorescence. FTIR shows a slight change in the secondary structure of rhGH in presence of the sugars as sucrose is more effective than trehalose. Fluorescence investigations also confirm the enhancements of folding of rhGH and fluorescein isothiocyanate (FITC)-rhGH in presence of sucrose (1.5-fold more than trehalose). Also, we studied sucrose's effect on the rete of aggregation of rhGH using spectroscopy of Congo red, and fluorescence imaging of thioflavin T (ThT)-treated samples. It can be suggested that sucrose facilitates the amyloid formation of rhGH during 20 days of incubation at 37°C. This study will help to understand the growth hormone structural behavior in the liquid state in the presence of sucrose and trehalose in vitro.
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Affiliation(s)
- Solmaz Kamrani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Parichehreh Yaghmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Nikkhah
- Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Dieplinger J, Pinto JT, Dekner M, Brachtl G, Paudel A. Impact of Different Saccharides on the In-Process Stability of a Protein Drug During Evaporative Drying: From Sessile Droplet Drying to Lab-Scale Spray Drying. Pharm Res 2023; 40:1283-1298. [PMID: 37012535 DOI: 10.1007/s11095-023-03498-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/05/2023] [Indexed: 04/05/2023]
Abstract
OBJECTIVES Solid biopharmaceutical products can circumvent lower temperature storage and transport and increase remote access with lower carbon emissions and energy consumption. Saccharides are known stabilizers in a solid protein produced via lyophilization and spray drying (SD). Thus, it is essential to understand the interactions between saccharides and proteins and the stabilization mechanism. METHODS A miniaturized single droplet drying (MD) method was developed to understand how different saccharides stabilize proteins during drying. We applied our MD to different aqueous saccharide-protein systems and transferred our findings to SD. RESULTS The poly- and oligosaccharides tend to destabilize the protein during drying. The oligosaccharide, Hydroxypropyl β-cyclodextrin (HPβCD) shows high aggregation at a high saccharide-to-protein molar ratio (S/P ratio) during MD, and the finding is supported by nanoDSF results. The polysaccharide, Dextran (DEX) leads to larger particles, whereas HPBCD leads to smaller particles. Furthermore, DEX is not able to stabilize the protein at higher S/P ratios either. In contrast, the disaccharide Trehalose Dihydrate (TD) does not increase or induce protein aggregation during the drying of the formulation. It can preserve the protein's secondary structure during drying, already at low concentrations. CONCLUSION During the drying of S/P formulations containing the saccharides TD and DEX, the MD approach could anticipate the in-process (in) stability of protein X at laboratory-scale SD. In contrast, for the systems with HPβCD, the results obtained by SD were contradictory to MD. This underlines that depending on the drying operation, careful consideration needs to be applied to the selection of saccharides and their ratios.
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Affiliation(s)
- Johanna Dieplinger
- Research Center for Pharmaceutical Engineering GmbH, Graz, Austria
- Institute of Process and Particle Engineering, Technical University of Graz, Graz, Austria
| | - Joana T Pinto
- Research Center for Pharmaceutical Engineering GmbH, Graz, Austria
| | | | | | - Amrit Paudel
- Research Center for Pharmaceutical Engineering GmbH, Graz, Austria.
- Institute of Process and Particle Engineering, Technical University of Graz, Graz, Austria.
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Gurel B, Berksoz M, Capkin E, Parlar A, Pala MC, Ozkan A, Capan Y, Daglikoca DE, Yuce M. Structural and Functional Analysis of CEX Fractions Collected from a Novel Avastin® Biosimilar Candidate and Its Innovator: A Comparative Study. Pharmaceutics 2022; 14:pharmaceutics14081571. [PMID: 36015197 PMCID: PMC9415858 DOI: 10.3390/pharmaceutics14081571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 02/01/2023] Open
Abstract
Avastin® is a humanized recombinant monoclonal antibody used to treat cancer by targeting VEGF-A to inhibit angiogenesis. SIMAB054, an Avastin® biosimilar candidate developed in this study, showed a different charge variant profile than its innovator. Thus, it is fractionated into acidic, main, and basic isoforms and collected physically by Cation Exchange Chromatography (CEX) for a comprehensive structural and functional analysis. The innovator product, fractionated into the same species and collected by the same method, is used as a reference for comparative analysis. Ultra-Performance Liquid Chromatography (UPLC) ESI-QToF was used to analyze the modifications leading to charge heterogeneities at intact protein and peptide levels. The C-terminal lysine clipping and glycosylation profiles of the samples were monitored by intact mAb analysis. The post-translational modifications, including oxidation, deamidation, and N-terminal pyroglutamic acid formation, were determined by peptide mapping analysis in the selected signal peptides. The relative binding affinities of the fractionated charge isoforms against the antigen, VEGF-A, and the neonatal receptor, FcRn, were revealed by Surface Plasmon Resonance (SPR) studies. The results show that all CEX fractions from the innovator product and the SIMAB054 shared the same structural variants, albeit in different ratios. Common glycoforms and post-translational modifications were the same, but at different percentages for some samples. The dissimilarities were mostly originating from the presence of extra C-term Lysin residues, which are prone to enzymatic degradation in the body, and thus they were previously assessed as clinically irrelevant. Another critical finding was the presence of different glyco proteoforms in different charge species, such as increased galactosylation in the acidic and afucosylation in the basic species. SPR characterization of the isolated charge variants further confirmed that basic species found in the CEX analyses of the biosimilar candidate were also present in the innovator product, although at lower amounts. The charge variants’ in vitro antigen- and neonatal receptor-binding activities varied amongst the samples, which could be further investigated in vivo with a larger sample set to reveal the impact on the pharmacokinetics of drug candidates. Minor structural differences may explain antigen-binding differences in the isolated charge variants, which is a key parameter in a comparability exercise. Consequently, such a biosimilar candidate may not comply with high regulatory standards unless the binding differences observed are justified and demonstrated not to have any clinical impact.
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Affiliation(s)
- Busra Gurel
- SUNUM Nanotechnology Research and Application Center, Sabanci University, Istanbul 34956, Turkey;
| | - Melike Berksoz
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
| | - Eda Capkin
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey;
| | - Ayhan Parlar
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey;
| | - Meltem Corbacioglu Pala
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
| | - Aylin Ozkan
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
| | - Yılmaz Capan
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
| | - Duygu Emine Daglikoca
- ILKO ARGEM Biotechnology R&D Center, Istanbul 34906, Turkey; (M.B.); (E.C.); (M.C.P.); (A.O.); (Y.C.)
- Correspondence: (D.E.D.); (M.Y.)
| | - Meral Yuce
- SUNUM Nanotechnology Research and Application Center, Sabanci University, Istanbul 34956, Turkey;
- Correspondence: (D.E.D.); (M.Y.)
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Liang J, Taylor SL, Baumert J, Alice Lee N. Development of a sensitive sandwich ELISA with broad species specificity for improved fish allergen detection. Food Chem 2022; 396:133656. [PMID: 35839724 DOI: 10.1016/j.foodchem.2022.133656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 06/09/2022] [Accepted: 07/06/2022] [Indexed: 11/04/2022]
Abstract
A sensitive Enzyme-linked Immunosorbent Assay (ELISA) with improved broad species specificity was developed for the detection of southern hemisphere fish residues in processed foods. The polyclonal antibodies were raised against parvalbumins from 13 fish species representing 7 fish orders selected for their molecular diversity and immunoreactivity profile. The optimized ELISA-2 (based on the rabbit capture antibody (RB#4) - sheep detection antibody (S2#4) pair) displayed an improved detection limit of 0.6 μg/L (3.7 μg of /kg). Our immunoreactivity-directed species selection approach in the strategized antibody production significantly improved the detection of no or weakly immunoreactive fish species previously not detected immunochemically. Of 37 commercially important fish species tested, the ELISA-2 could detect 28 fish species (76%). The optimized sample extraction with a buffer additive achieved good protein recoveries of 87.2 - 117.3% (within the AOAC recommended range). The ELISA-2 was able to detect fish residues in five highly processed food products.
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Affiliation(s)
- Ji Liang
- ARC Training Centre for Advanced Technologies in Food Manufacture, School of Chemical Engineering, University of New South Wales, New South Wales, Australia
| | - Stephen L Taylor
- Food Allergy Research and Resource Program, Department of Food Science and Technology, University of Nebraska-Lincoln, Nebraska, United States
| | - Joseph Baumert
- Food Allergy Research and Resource Program, Department of Food Science and Technology, University of Nebraska-Lincoln, Nebraska, United States
| | - N Alice Lee
- ARC Training Centre for Advanced Technologies in Food Manufacture, School of Chemical Engineering, University of New South Wales, New South Wales, Australia.
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Luther DC, Nagaraj H, Goswami R, Çiçek YA, Jeon T, Gopalakrishnan S, Rotello VM. Direct Cytosolic Delivery of Proteins Using Lyophilized and Reconstituted Polymer-Protein Assemblies. Pharm Res 2022; 39:1197-1204. [PMID: 35297498 PMCID: PMC10587898 DOI: 10.1007/s11095-022-03226-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/04/2022] [Indexed: 10/18/2022]
Abstract
PURPOSE Cytosolic delivery of proteins accesses intracellular targets for chemotherapy and immunomodulation. Current delivery systems utilize inefficient endosomal pathways of uptake and escape that lead to degradation of delivered cargo. Cationic poly(oxanorbornene)imide (PONI) polymers enable highly efficient cytosolic delivery of co-engineered proteins, but aggregation and denaturation in solution limits shelf life. In the present study we evaluate polymer-protein nanocomposite vehicles as candidates for lyophilization and point-of-care resuspension to provide a transferrable technology for cytosolic protein delivery. METHODS Self-assembled nanocomposites of engineered poly(glutamate)-tagged (E-tagged) proteins and guanidinium-functionalized PONI homopolymers were generated, lyophilized, and stored for 2 weeks. After reconstitution and delivery, cytosolic access of E-tagged GFP cargo (GFPE15) was assessed through diffuse cytosolic and nuclear fluorescence, and cell killing with chemotherapeutic enzyme Granzyme A (GrAE10). Efficiency was quantified between freshly prepared and lyophilized samples. RESULTS Reconstituted nanocomposites retained key structural features of freshly prepared assemblies, with minimal loss of material. Cytosolic delivery (> 80% efficiency of freshly prepared nanocomposites) of GFPE15 was validated in several cell lines, with intracellular access validated and quantified through diffusion into the nucleus. Delivery of GrAE10 elicited significant tumorigenic cell death. Intracellular access of cytotoxic protein was validated through cell viability. CONCLUSION Reconstituted nanocomposites achieved efficient cytosolic delivery of protein cargo and demonstrated therapeutic applicability with delivery of GrAE10. Overall, this strategy represents a versatile and highly translatable method for cytosolic delivery of proteins.
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Affiliation(s)
- David C Luther
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Harini Nagaraj
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Ritabrita Goswami
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Yağız Anıl Çiçek
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Taewon Jeon
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Sanjana Gopalakrishnan
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA.
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9
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Isaev N, Steinhoff HJ. Protein and solutes freeze-concentration in water/glycerol mixtures revealed by pulse EPR. Eur J Pharm Biopharm 2021; 169:44-51. [PMID: 34534655 DOI: 10.1016/j.ejpb.2021.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022]
Abstract
Lyophilization can extend protein drugs stability and shelf life, but it also can lead to protein degradation in some cases. The development of safe freeze-drying approaches for sensitive proteins requires a better understanding of lyophilization on the molecular level. The evaluation of the freezing process and its impact on the protein environment in the nm scale is challenging because feasible experimental methods are scarce. In the present work we apply pulse EPR as a tool to study the local concentrations of the solute in the 20 nm range and of the solvent in the 1 nm range for a spin labeled 27 kDa monomeric green fluorescent protein, mEGFP, and the 172 Da TEMPOL spin probe, frozen in different water/glycerol-d5 mixtures. For average glycerol volume fractions, φgly-d5avg, ≥ 0.4 we observed transparent glassy media; the local concentration and the 1 nm solvent shell of TEMPOL and the protein correspond to those of a uniform vitrified glass. At φgly-d5avg ≤ 0.3 we observed partial ice crystallization, which led to ice exclusion of glycerol and TEMPOL with freeze-concentration up to the glycerol maximal-freeze local volume fraction, φgly-d5loc, of 0.64. The protein concentration and its shell behavior was similar except for the lowest φgly-d5avg (0.1), which showed a 4.7-fold freeze-concentration factor compared to sevenfold for TEMPOL, and also a smaller φgly-d5loc. We explain this behavior with an increased probability for proteins to get stuck in the ice phase during fast freezing at higher freeze-concentration and the related large-scale mass transfer.
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Affiliation(s)
- Nikolay Isaev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Novosibirsk, Russia.
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10
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Li Z, Zhao W, Ma S, Li Z, Yao Y, Fei T. A chemical-enhanced system for CRISPR-Based nucleic acid detection. Biosens Bioelectron 2021; 192:113493. [PMID: 34271398 PMCID: PMC8443255 DOI: 10.1016/j.bios.2021.113493] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/27/2021] [Accepted: 07/06/2021] [Indexed: 12/19/2022]
Abstract
The CRISPR-based nucleic acid detection systems have shown great potential for point-of-care testing of viral pathogens, especially in the context of COVID-19 pandemic. Here we optimize several key parameters of reaction chemistry and develop a Chemical Enhanced CRISPR Detection system for nucleic acid (termed CECRID). For the Cas12a/Cas13a-based signal detection phase, we determine buffer conditions and substrate range for optimal detection performance, and reveal a crucial role of bovine serum albumin in enhancing trans-cleavage activity of Cas12a/Cas13a effectors. By comparing several chemical additives, we find that addition of L-proline can secure or enhance Cas12a/Cas13a detection capability. For isothermal amplification phase with typical LAMP and RPA methods, inclusion of L-proline can also enhance specific target amplification as determined by CRISPR detection. Using SARS-CoV-2 pseudovirus, we demonstrate CECRID has enhanced detection sensitivity over chemical additive-null method with either fluorescence or lateral flow strip readout. Thus, CECRID provides an improved detection power and system robustness, and helps to develop enhanced reagent formula or test kit towards practical application of CRISPR-based diagnostics.
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Affiliation(s)
- Zihan Li
- College of Life and Health Sciences, Northeastern University, Shenyang, 110819, People's Republic of China; Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, 110819, People's Republic of China
| | - Wenchang Zhao
- College of Life and Health Sciences, Northeastern University, Shenyang, 110819, People's Republic of China; Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, 110819, People's Republic of China
| | - Shixin Ma
- College of Life and Health Sciences, Northeastern University, Shenyang, 110819, People's Republic of China; Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, 110819, People's Republic of China
| | - Zexu Li
- College of Life and Health Sciences, Northeastern University, Shenyang, 110819, People's Republic of China; Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, 110819, People's Republic of China
| | - Yingjia Yao
- College of Life and Health Sciences, Northeastern University, Shenyang, 110819, People's Republic of China; Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, 110819, People's Republic of China
| | - Teng Fei
- College of Life and Health Sciences, Northeastern University, Shenyang, 110819, People's Republic of China; Key Laboratory of Data Analytics and Optimization for Smart Industry (Northeastern University), Ministry of Education, Shenyang, 110819, People's Republic of China.
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11
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Efficient Amino Donor Recycling in Amination Reactions: Development of a New Alanine Dehydrogenase in Continuous Flow and Dialysis Membrane Reactors. Catalysts 2021. [DOI: 10.3390/catal11040520] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Transaminases have arisen as one of the main biocatalysts for amine production but despite their many advantages, their stability is still a concern for widespread application. One of the reasons for their instability is the need to use an excess of the amino donor when trying to synthesise amines with unfavourable equilibria. To circumvent this, recycling systems for the amino donor, such as amino acid dehydrogenases or aldolases, have proved useful to push the equilibria while avoiding high amino donor concentrations. In this work, we report the use of a new alanine dehydrogenase from the halotolerant bacteria Halomonas elongata which exhibits excellent stability to different cosolvents, combined with the well characterised CbFDH as a recycling system of L-alanine for the amination of three model substrates with unfavourable equilibria. In a step forward, the amino donor recycling system has been co-immobilised and used in flow with success as well as re-used as a dialysis enclosed system for the amination of an aromatic aldehyde.
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12
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Bacteriophage-derived endolysins to target gram-negative bacteria. Int J Pharm 2020; 589:119833. [PMID: 32877733 DOI: 10.1016/j.ijpharm.2020.119833] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
Bacteriophage-encoded endolysins (lysins) have emerged as a novel class of antibacterial agents to combat the surging antibiotic resistance. Lysins have specific structures and mechanisms to exert antibacterial effect against both Gram-positive (G+ve) and Gram-negative (G-ve) bacteria. However, its use against G-ve bacteria is limited because the outer membrane (OM) of G-ve bacteria hinders the permeation of exogenously applied lysins. Besides identifying lysins with intrinsic OM permeability, several other approaches including combining lysins with outer membrane permeabilizers (OMPs), protein engineering and formulating with nanocarriers have been proposed to enhance the permeability and activity of lysins. In the present review, we summarize strategies that have been developed to enable lysins to target G-ve bacteria in the past decade. While lysins demonstrates clear potential in managing bacterial infections caused by the drug-resistant G-ve bacteria, there are still challenges hindering their translation into clinical settings, including safety issues with OMP use, low efficiency against stationary phase bacteria and problems in stability. The applicability of protein engineering and formulation sciences to improve enzyme stability, and combination therapy with other classes of antibacterial agents to maximize the therapeutic potential have also been reviewed.
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Magnetic Nanoclusters Coated with Albumin, Casein, and Gelatin: Size Tuning, Relaxivity, Stability, Protein Corona, and Application in Nuclear Magnetic Resonance Immunoassay. NANOMATERIALS 2019; 9:nano9091345. [PMID: 31546937 PMCID: PMC6781099 DOI: 10.3390/nano9091345] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 02/08/2023]
Abstract
The surface functionalization of magnetic nanoparticles improves their physicochemical properties and applicability in biomedicine. Natural polymers, including proteins, are prospective coatings capable of increasing the stability, biocompatibility, and transverse relaxivity (r2) of magnetic nanoparticles. In this work, we functionalized the nanoclusters of carbon-coated iron nanoparticles with four proteins: bovine serum albumin, casein, and gelatins A and B, and we conducted a comprehensive comparative study of their properties essential to applications in biosensing. First, we examined the influence of environmental parameters on the size of prepared nanoclusters and synthesized protein-coated nanoclusters with a tunable size. Second, we showed that protein coating does not significantly influence the r2 relaxivity of clustered nanoparticles; however, the uniform distribution of individual nanoparticles inside the protein coating facilitates increased relaxivity. Third, we demonstrated the applicability of the obtained nanoclusters in biosensing by the development of a nuclear-magnetic-resonance-based immunoassay for the quantification of antibodies against tetanus toxoid. Fourth, the protein coronas of nanoclusters were studied using SDS-PAGE and Bradford protein assay. Finally, we compared the colloidal stability at various pH values and ionic strengths and in relevant complex media (i.e., blood serum, plasma, milk, juice, beer, and red wine), as well as the heat stability, resistance to proteolytic digestion, and shelf-life of protein-coated nanoclusters.
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14
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Abd Ellah NH, Abd El‐Aziz FEA, Abouelmagd SA, Abd El‐Hamid BN, Hetta HF. Spidroin in carbopol‐based gel promotes wound healing in earthworm's skin model. Drug Dev Res 2019; 80:1051-1061. [DOI: 10.1002/ddr.21583] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/21/2019] [Accepted: 07/25/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Noura H. Abd Ellah
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, Medical Sciences BuildingUniversity of Cincinnati Cincinnati Ohio USA
- Department of Pharmaceutics, Faculty of PharmacyAssiut University Assiut Egypt
| | | | - Sara A. Abouelmagd
- Department of Pharmaceutics, Faculty of PharmacyAssiut University Assiut Egypt
| | | | - Helal F. Hetta
- Department of Internal MedicineUniversity of Cincinnati College of Medicine Cincinnati Ohio USA
- Department of Medical Microbiology and Immunology, Faculty of MedicineAssiut University Assiut Egypt
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15
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Liu Z, Yang C, Huang J, Ciampalini G, Li J, García Sakai V, Tyagi M, O'Neill H, Zhang Q, Capaccioli S, Ngai KL, Hong L. Direct Experimental Characterization of Contributions from Self-Motion of Hydrogen and from Interatomic Motion of Heavy Atoms to Protein Anharmonicity. J Phys Chem B 2018; 122:9956-9961. [PMID: 30295486 DOI: 10.1021/acs.jpcb.8b09355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One fundamental challenge in biophysics is to understand the connection between protein dynamics and its function. Part of the difficulty arises from the fact that proteins often present local atomic motions and collective dynamics on the same time scales, and challenge the experimental identification and quantification of different dynamic modes. Here, by taking lyophilized proteins as the example, we combined deuteration technique and neutron scattering to separate and characterize the self-motion of hydrogen and the collective interatomic motion of heavy atoms (C, O, N) in proteins on the pico-to-nanosecond time scales. We found that hydrogen atoms present an instrument-resolution-dependent onset for anharmonic motions, which can be ascribed to the thermal activation of local side-group motions. However, the protein heavy atoms exhibit an instrument-resolution-independent anharmonicity around 200 K, which results from unfreezing of the relaxation of the protein structures on the laboratory equilibrium time (100-1000 s), softening of the entire bio-macromolecules.
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Affiliation(s)
| | | | | | - Gaia Ciampalini
- Dipartimento di Fisica "E. Fermi" , Università di Pisa and Istituto per Processi Chimico-Fisici-Consiglio Nazionale delle Ricerche , Largo Pontecorvo 3 , Pisa 56127 , Italy
| | | | - Victoria García Sakai
- ISIS Neutron and Muon Facility , Rutherford Appleton Laboratory, Science & Technology Facilities Council , Didcot OX11 0QX , United Kingdom
| | - Madhusudan Tyagi
- National Institute of Standards and Technology (NIST) , NIST Center for Neutron Research , Gaithersburg , Maryland 20899 , United States.,Department of Materials Science and Engineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Hugh O'Neill
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37931 , United States
| | - Qiu Zhang
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37931 , United States
| | - Simone Capaccioli
- Dipartimento di Fisica "E. Fermi" , Università di Pisa and Istituto per Processi Chimico-Fisici-Consiglio Nazionale delle Ricerche , Largo Pontecorvo 3 , Pisa 56127 , Italy
| | - K L Ngai
- Dipartimento di Fisica "E. Fermi" , Università di Pisa and Istituto per Processi Chimico-Fisici-Consiglio Nazionale delle Ricerche , Largo Pontecorvo 3 , Pisa 56127 , Italy
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16
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McGuinness KN, Pan W, Sheridan RP, Murphy G, Crespo A. Role of simple descriptors and applicability domain in predicting change in protein thermostability. PLoS One 2018; 13:e0203819. [PMID: 30192891 PMCID: PMC6128648 DOI: 10.1371/journal.pone.0203819] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/28/2018] [Indexed: 01/07/2023] Open
Abstract
The melting temperature (Tm) of a protein is the temperature at which half of the protein population is in a folded state. Therefore, Tm is a measure of the thermostability of a protein. Increasing the Tm of a protein is a critical goal in biotechnology and biomedicine. However, predicting the change in melting temperature (dTm) due to mutations at a single residue is difficult because it depends on an intricate balance of forces. Existing methods for predicting dTm have had similar levels of success using generally complex models. We find that training a machine learning model with a simple set of easy to calculate physicochemical descriptors describing the local environment of the mutation performed as well as more complicated machine learning models and is 2-6 orders of magnitude faster. Importantly, unlike in most previous publications, we perform a blind prospective test on our simple model by designing 96 variants of a protein not in the training set. Results from retrospective and prospective predictions reveal the limited applicability domain of each model. This study highlights the current deficiencies in the available dTm dataset and is a call to the community to systematically design a larger and more diverse experimental dataset of mutants to prospectively predict dTm with greater certainty.
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Affiliation(s)
- Kenneth N. McGuinness
- Modeling and Informatics, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Weilan Pan
- Biochemical Engineering and Structure, Merck & Co., Inc., Rahway, New Jersey, United States of America
| | - Robert P. Sheridan
- Modeling and Informatics, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Grant Murphy
- Biochemical Engineering and Structure, Merck & Co., Inc., Rahway, New Jersey, United States of America
| | - Alejandro Crespo
- Modeling and Informatics, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
- * E-mail:
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17
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Guidelines to reach high-quality purified recombinant proteins. Appl Microbiol Biotechnol 2017; 102:81-92. [DOI: 10.1007/s00253-017-8623-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/24/2017] [Accepted: 10/27/2017] [Indexed: 10/18/2022]
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18
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Silva C, Martins M, Jing S, Fu J, Cavaco-Paulo A. Practical insights on enzyme stabilization. Crit Rev Biotechnol 2017; 38:335-350. [PMID: 28764566 DOI: 10.1080/07388551.2017.1355294] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Enzymes are efficient catalysts designed by nature to work in physiological environments of living systems. The best operational conditions to access and convert substrates at the industrial level are different from nature and normally extreme. Strategies to isolate enzymes from extremophiles can redefine new operational conditions, however not always solving all industrial requirements. The stability of enzymes is therefore a key issue on the implementation of the catalysts in industrial processes which require the use of extreme environments that can undergo enzyme instability. Strategies for enzyme stabilization have been exhaustively reviewed, however they lack a practical approach. This review intends to compile and describe the most used approaches for enzyme stabilization highlighting case studies in a practical point of view.
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Affiliation(s)
- Carla Silva
- a Centre of Biological Engineering (CEB) , University of Minho , Braga , Portugal
| | - Madalena Martins
- a Centre of Biological Engineering (CEB) , University of Minho , Braga , Portugal
| | - Su Jing
- b International Joint Research Laboratory for Textile and Fiber Bioprocesses , Jiangnan University , Wuxi , China
| | - Jiajia Fu
- c Key Laboratory of Science and Technology of Eco-Textiles , Ministry of Education, Jiangnan University , Wuxi , Jiangsu , China
| | - Artur Cavaco-Paulo
- a Centre of Biological Engineering (CEB) , University of Minho , Braga , Portugal.,b International Joint Research Laboratory for Textile and Fiber Bioprocesses , Jiangnan University , Wuxi , China
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19
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Karthikeyan S, Kurt Z, Pandey G, Spain JC. Immobilized Biocatalyst for Detection and Destruction of the Insensitive Explosive, 2,4-Dinitroanisole (DNAN). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:11193-11199. [PMID: 27617621 DOI: 10.1021/acs.est.6b03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Accurate and convenient detection of explosive components is vital for a wide spectrum of applications ranging from national security and demilitarization to environmental monitoring and restoration. With the increasing use of DNAN as a replacement for 2,4,6-trinitrotoluene (TNT) in insensitive explosive formulations, there has been a growing interest in strategies to minimize its release and to understand and predict its behavior in the environment. Consequently, a convenient tool for its detection and destruction could enable development of more effective decontamination and demilitarization strategies. Biosensors and biocatalysts have limited applicability to the more traditional explosives because of the inherent limitations of the relevant enzymes. Here, we report a highly specific, convenient and robust biocatalyst based on a novel ether hydrolase enzyme, DNAN demethylase (that requires no cofactors), from a Nocardioides strain that can mineralize DNAN. Biogenic silica encapsulation was used to stabilize the enzyme and enable it to be packed into a model microcolumn for application as a biosensor or as a bioreactor for continuous destruction of DNAN. The immobilized enzyme was stable and not inhibited by other insensitive munitions constituents. An alternative method for DNAN detection involved coating the encapsulated enzyme on cellulose filter paper. The hydrolase based biocatalyst could provide the basis for a wide spectrum of applications including detection, identification, destruction or inertion of explosives containing DNAN (demilitarization operations), and for environmental restorations.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Civil and Environmental Engineering, Georgia Institute of Technology , 311 Ferst Drive, Atlanta, Georgia 30332, United States
| | - Zohre Kurt
- Department of Civil and Environmental Engineering, Georgia Institute of Technology , 311 Ferst Drive, Atlanta, Georgia 30332, United States
- Institute of Scientific Research and High Technology Services , Calle Pullpn, Panamá, Panama
| | - Gunjan Pandey
- CSIRO Land and Water , Clunies Ross Street, Acton, Australian Capital Territory 2615, Australia
| | - Jim C Spain
- Department of Civil and Environmental Engineering, Georgia Institute of Technology , 311 Ferst Drive, Atlanta, Georgia 30332, United States
- Center for Environmental Diagnostics & Bioremediation, University of West Florida , 11000 University Parkway, Pensacola, Florida 32514-5751, United States
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20
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Yu X, Bogaert L, Hu R, Bals O, Grimi N, Vorobiev E. A combined coagulation–ultrafiltration method for enhanced separation of proteins and polyphenols. SEP SCI TECHNOL 2016. [DOI: 10.1080/01496395.2016.1141957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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21
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Lew MH, Lim RLH. Expression of a codon-optimised recombinant Ara h 2.02 peanut allergen in Escherichia coli. Appl Microbiol Biotechnol 2015; 100:661-71. [DOI: 10.1007/s00253-015-6953-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/12/2015] [Accepted: 08/22/2015] [Indexed: 10/23/2022]
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22
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Li H, Munzar JD, Ng A, Juncker D. A versatile snap chip for high-density sub-nanoliter chip-to-chip reagent transfer. Sci Rep 2015; 5:11688. [PMID: 26148566 PMCID: PMC4493572 DOI: 10.1038/srep11688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/05/2015] [Indexed: 01/15/2023] Open
Abstract
The coordinated delivery of minute amounts of different reagents is important for microfluidics and microarrays, but is dependent on advanced equipment such as microarrayers. Previously, we developed the snap chip for the direct transfer of reagents, thus realizing fluidic operations by only manipulating microscope slides. However, owing to the misalignment between arrays spotted on different slides, millimeter spacing was needed between spots and the array density was limited. In this work, we have developed a novel double transfer method and have transferred 625 spots cm(-2), corresponding to >10000 spots for a standard microscope slide. A user-friendly snapping system was manufactured to make liquid handling straightforward. Misalignment, which for direct transfer ranged from 150-250 μm, was reduced to <40 μm for double transfer. The snap chip was used to quantify 50 proteins in 16 samples simultaneously, yielding limits of detection in the pg/mL range for 35 proteins. The versatility of the snap chip is illustrated with a 4-plex homogenous enzyme inhibition assay analyzing 128 conditions with precise timing. The versatility and high density of the snap chip with double transfer allows for the development of high throughput reagent transfer protocols compatible with a variety of applications.
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Affiliation(s)
- Huiyan Li
- Biomedical Engineering Department, McGill University, Montréal, QC, H3A 0G1, Canada
- McGill University and Genome Quebec Innovation Centre, McGill University, Montréal, QC, H3A 0G1, Canada
| | - Jeffrey D. Munzar
- Biomedical Engineering Department, McGill University, Montréal, QC, H3A 0G1, Canada
- McGill University and Genome Quebec Innovation Centre, McGill University, Montréal, QC, H3A 0G1, Canada
| | - Andy Ng
- Biomedical Engineering Department, McGill University, Montréal, QC, H3A 0G1, Canada
- McGill University and Genome Quebec Innovation Centre, McGill University, Montréal, QC, H3A 0G1, Canada
| | - David Juncker
- Biomedical Engineering Department, McGill University, Montréal, QC, H3A 0G1, Canada
- McGill University and Genome Quebec Innovation Centre, McGill University, Montréal, QC, H3A 0G1, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 0G1, Canada
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23
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Walsh G. Protein Purification and Characterization. Proteins 2015. [DOI: 10.1002/9781119117599.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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LaCava J, Molloy KR, Taylor MS, Domanski M, Chait BT, Rout MP. Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives. Biotechniques 2015; 58:103-19. [PMID: 25757543 PMCID: PMC4465938 DOI: 10.2144/000114262] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/17/2015] [Indexed: 01/13/2023] Open
Abstract
Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with the co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, high specificity reagents to target and capture proteins of interest along with specifically associated proteins from cell extracts. Affinity capture coupled to mass spectrometry (MS)-based proteomic analyses has enabled the isolation and characterization of a wide range of endogenous protein complexes. Here, we outline effective procedures for the affinity capture of protein complexes, highlighting best practices and common pitfalls.
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Affiliation(s)
- John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Institute for Systems Genetics, New York University School of Medicine, New York, NY
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Martin S. Taylor
- High Throughput Biology Center and Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michal Domanski
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
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25
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Raynal B, Lenormand P, Baron B, Hoos S, England P. Quality assessment and optimization of purified protein samples: why and how? Microb Cell Fact 2014; 13:180. [PMID: 25547134 PMCID: PMC4299812 DOI: 10.1186/s12934-014-0180-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/10/2014] [Indexed: 01/27/2023] Open
Abstract
Purified protein quality control is the final and critical check-point of any protein production process. Unfortunately, it is too often overlooked and performed hastily, resulting in irreproducible and misleading observations in downstream applications. In this review, we aim at proposing a simple-to-follow workflow based on an ensemble of widely available physico-chemical technologies, to assess sequentially the essential properties of any protein sample: purity and integrity, homogeneity and activity. Approaches are then suggested to optimize the homogeneity, time-stability and storage conditions of purified protein preparations, as well as methods to rapidly evaluate their reproducibility and lot-to-lot consistency.
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Affiliation(s)
- Bertrand Raynal
- Institut Pasteur, Biophysics of Macromolecules and their Interactions, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France.
- CNRS-UMR3528, Institut Pasteur, Departement of Structural Biology and Chemistry, Paris, France.
| | - Pascal Lenormand
- Institut Pasteur, Biophysics of Macromolecules and their Interactions, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France.
- CNRS-UMR3528, Institut Pasteur, Departement of Structural Biology and Chemistry, Paris, France.
| | - Bruno Baron
- Institut Pasteur, Biophysics of Macromolecules and their Interactions, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France.
- CNRS-UMR3528, Institut Pasteur, Departement of Structural Biology and Chemistry, Paris, France.
| | - Sylviane Hoos
- Institut Pasteur, Biophysics of Macromolecules and their Interactions, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France.
- CNRS-UMR3528, Institut Pasteur, Departement of Structural Biology and Chemistry, Paris, France.
| | - Patrick England
- Institut Pasteur, Biophysics of Macromolecules and their Interactions, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France.
- CNRS-UMR3528, Institut Pasteur, Departement of Structural Biology and Chemistry, Paris, France.
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Rapid method using two microbial enzymes for detection of L-abrine in food as a marker for the toxic protein abrin. Appl Environ Microbiol 2014; 81:1610-5. [PMID: 25527549 DOI: 10.1128/aem.03492-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abrin is a toxic protein produced by the ornamental plant Abrus precatorius, and it is of concern as a biothreat agent. The small coextracting molecule N-methyl-l-tryptophan (l-abrine) is specific to members of the genus Abrus and thus can be used as a marker for the presence or ingestion of abrin. Current methods for the detection of abrin or l-abrine in foods and other matrices require complex sample preparation and expensive instrumentation. To develop a fast and portable method for the detection of l-abrine in beverages and foods, the Escherichia coli proteins N-methyltryptophan oxidase (MTOX) and tryptophanase were expressed and purified. The two enzymes jointly degraded l-abrine to products that included ammonia and indole, and colorimetric assays for the detection of those analytes in beverage and food samples were evaluated. An indole assay using a modified version of Ehrlich's/Kovac's reagent was more sensitive and less subject to negative interferences from components in the samples than the Berthelot ammonia assay. The two enzymes were added into food and beverage samples spiked with l-abrine, and indole was detected as a degradation product, with the visual lower detection limit being 2.5 to 10.0 μM (∼0.6 to 2.2 ppm) l-abrine in the samples tested. Results could be obtained in as little as 15 min. Sample preparation was limited to pH adjustment of some samples. Visual detection was found to be about as sensitive as detection with a spectrophotometer, especially in milk-based matrices.
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Stabilization of therapeutic proteins in aqueous solutions and freeze-dried solids: an overview. Methods Mol Biol 2014; 1129:435-41. [PMID: 24648092 DOI: 10.1007/978-1-62703-977-2_31] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Intrinsic chemical instability and physical instability of therapeutic proteins require appropriate formulations and processes to ensure their efficacy and safety. Recent concerns on possible immunogenicity of the structurally altered protein molecules emphasize relevance of the product quality. Advances in the protein and material researches enable rational design of the aqueous solution and solid protein formulations. This chapter describes the basic process to develop the formulations and choice of excipients that protect the proteins from various stresses during the manufacturing and storage.
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28
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Pérez-Pérez ME, Zaffagnini M, Marchand CH, Crespo JL, Lemaire SD. The yeast autophagy protease Atg4 is regulated by thioredoxin. Autophagy 2014; 10:1953-64. [PMID: 25483965 DOI: 10.4161/auto.34396] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Autophagy is a membrane-trafficking process whereby double-membrane vesicles called autophagosomes engulf and deliver intracellular material to the vacuole for degradation. Atg4 is a cysteine protease with an essential function in autophagosome formation. Mounting evidence suggests that reactive oxygen species may play a role in the control of autophagy and could regulate Atg4 activity but the precise mechanisms remain unclear. In this study, we showed that reactive oxygen species activate autophagy in the model yeast Saccharomyces cerevisiae and unraveled the molecular mechanism by which redox balance controls Atg4 activity. A combination of biochemical assays, redox titrations, and site-directed mutagenesis revealed that Atg4 is regulated by oxidoreduction of a single disulfide bond between Cys338 and Cys394. This disulfide has a low redox potential and is very efficiently reduced by thioredoxin, suggesting that this oxidoreductase plays an important role in Atg4 regulation. Accordingly, we found that autophagy activation by rapamycin was more pronounced in a thioredoxin mutant compared with wild-type cells. Moreover, in vivo studies indicated that Cys338 and Cys394 are required for the proper regulation of autophagosome biogenesis, since mutation of these cysteines resulted in increased recruitment of Atg8 to the phagophore assembly site. Thus, we propose that the fine-tuning of Atg4 activity depending on the intracellular redox state may regulate autophagosome formation.
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Key Words
- ATG, autophagy-related
- Ape1, aminopeptidase I
- Asc, ascorbate
- Atg4
- Cvt, cytoplasm-to-vacuole targeting
- DTNB, 5, 5′-dithiobis (2-nitro-benzoic acid)
- DTT, dithiothreitol
- DTTox, oxidized DTT
- DTTred, reduced DTT
- Eh, redox potential
- Em, midpoint redox potential
- GSH, reduced glutathione
- GSNO, S-nitrosoglutathione
- GSSG, oxidized glutathione
- Gsr, glutathione reductase
- IAM, iodoacetamide
- NEM, N-ethylmaleimide
- PAS, phagophore assembly site
- PE, phosphatidylethanolamine
- PTM, post-translational modification
- ROS, reactive oxygen species
- SD, synthetic minimal medium
- Trr1, thioredoxin reductase 1
- Trx1, thioredoxin 1
- YPD, yeast peptone dextrose
- autophagy
- phagophore assembly site
- rap, rapamycin
- redox regulation
- thioredoxin
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Affiliation(s)
- María Esther Pérez-Pérez
- a Centre National de la Recherche Scientifique; UMR8226; Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes; Institut de Biologie Physico-Chimique ; Paris , France
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29
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Abstract
INTRODUCTION Proteins are effective biotherapeutics with applications in diverse ailments. Despite being specific and potent, their full clinical potential has not yet been realized. This can be attributed to short half-lives, complex structures, poor in vivo stability, low permeability, frequent parenteral administrations and poor adherence to treatment in chronic diseases. A sustained release system, providing controlled release of proteins, may overcome many of these limitations. AREAS COVERED This review focuses on recent development in approaches, especially polymer-based formulations, which can provide therapeutic levels of proteins over extended periods. Advances in particulate, gel-based formulations and novel approaches for extended protein delivery are discussed. Emphasis is placed on dosage form, method of preparation, mechanism of release and stability of biotherapeutics. EXPERT OPINION Substantial advancements have been made in the field of extended protein delivery via various polymer-based formulations over last decade despite the unique delivery-related challenges posed by protein biologics. A number of injectable sustained-release formulations have reached market. However, therapeutic application of proteins is still hampered by delivery-related issues. A large number of protein molecules are under clinical trials, and hence, there is an urgent need to develop new methods to deliver these highly potent biologics.
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Affiliation(s)
- Ravi Vaishya
- University of Missouri-Kansas City, Pharmaceutical Sciences , Kansas City, MO , USA
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30
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Shin DJ, Wang TH. Magnetic droplet manipulation platforms for nucleic acid detection at the point of care. Ann Biomed Eng 2014; 42:2289-302. [PMID: 25008142 DOI: 10.1007/s10439-014-1060-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/19/2014] [Indexed: 12/13/2022]
Abstract
This review summarizes recent developments in the use of magnetically actuated droplets in point-of-care molecular diagnostic platforms. We discuss the fundamentals of magnetic droplet manipulation and the various modes of actuation. The balance of forces acting on a droplet during transport and particle extraction, as well as the devices and instrumentation developed to perform these operations will be presented and discussed. Furthermore, we review some of the recent advances on the diagnostic applications of platforms utilizing magnetic manipulation for genetic assessment of biological samples.
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Affiliation(s)
- Dong Jin Shin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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31
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Structure-based prediction of asparagine and aspartate degradation sites in antibody variable regions. PLoS One 2014; 9:e100736. [PMID: 24959685 PMCID: PMC4069079 DOI: 10.1371/journal.pone.0100736] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/30/2014] [Indexed: 12/29/2022] Open
Abstract
Monoclonal antibodies (mAbs) and proteins containing antibody domains are the most prevalent class of biotherapeutics in diverse indication areas. Today, established techniques such as immunization or phage display allow for an efficient generation of new mAbs. Besides functional properties, the stability of future therapeutic mAbs is a key selection criterion which is essential for the development of a drug candidate into a marketed product. Therapeutic proteins may degrade via asparagine (Asn) deamidation and aspartate (Asp) isomerization, but the factors responsible for such degradation remain poorly understood. We studied the structural properties of a large, uniform dataset of Asn and Asp residues in the variable domains of antibodies. Their structural parameters were correlated with the degradation propensities measured by mass spectrometry. We show that degradation hotspots can be characterized by their conformational flexibility, the size of the C-terminally flanking amino acid residue, and secondary structural parameters. From these results we derive an accurate in silico prediction method for the degradation propensity of both Asn and Asp residues in the complementarity-determining regions (CDRs) of mAbs.
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Kim M, Gkikas M, Huang A, Kang JW, Suthiwangcharoen N, Nagarajan R, Olsen BD. Enhanced activity and stability of organophosphorus hydrolase via interaction with an amphiphilic polymer. Chem Commun (Camb) 2014; 50:5345-8. [PMID: 24558645 PMCID: PMC4059822 DOI: 10.1039/c3cc47675h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple approach to enhancing the activity and stability of organophosphorus hydrolase (OPH) is developed based on interactions between the hydrophobic poly(propylene oxide) (PPO) block of amphiphilic Pluronics and the enzyme. This strategy provides an efficient route to new formulations for decontaminating organophosphate neurotoxins.
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Affiliation(s)
- Minkyu Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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33
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Hood JL, Scott MJ, Wickline SA. Maximizing exosome colloidal stability following electroporation. Anal Biochem 2013; 448:41-9. [PMID: 24333249 DOI: 10.1016/j.ab.2013.12.001] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 11/25/2013] [Accepted: 12/02/2013] [Indexed: 12/21/2022]
Abstract
Development of exosome-based semisynthetic nanovesicles for diagnostic and therapeutic purposes requires novel approaches to load exosomes with cargo. Electroporation has previously been used to load exosomes with RNA. However, investigations into exosome colloidal stability following electroporation have not been considered. Herein, we report the development of a unique trehalose pulse media (TPM) that minimizes exosome aggregation following electroporation. Dynamic light scattering (DLS) and RNA absorbance were employed to determine the extent of exosome aggregation and electroextraction post electroporation in TPM compared to common PBS pulse media or sucrose pulse media (SPM). Use of TPM to disaggregate melanoma exosomes post electroporation was dependent on both exosome concentration and electric field strength. TPM maximized exosome dispersal post electroporation for both homogenous B16 melanoma and heterogeneous human serum-derived populations of exosomes. Moreover, TPM enabled heavy cargo loading of melanoma exosomes with 5nm superparamagnetic iron oxide nanoparticles (SPION5) while maintaining original exosome size and minimizing exosome aggregation as evidenced by transmission electron microscopy. Loading exosomes with SPION5 increased exosome density on sucrose gradients. This provides a simple, label-free means of enriching exogenously modified exosomes and introduces the potential for MRI-driven theranostic exosome investigations in vivo.
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Affiliation(s)
- Joshua L Hood
- Consortium for Translational Research in Advanced Imaging and Nanomedicine (C-TRAIN), Cardiovascular Division, Department of Medicine, Washington University School of Medicine, 4320 Forest Park Avenue, Suite 101, Campus Box 8215, St. Louis, MO 63108, USA.
| | - Michael J Scott
- Consortium for Translational Research in Advanced Imaging and Nanomedicine (C-TRAIN), Cardiovascular Division, Department of Medicine, Washington University School of Medicine, 4320 Forest Park Avenue, Suite 101, Campus Box 8215, St. Louis, MO 63108, USA.
| | - Samuel A Wickline
- Consortium for Translational Research in Advanced Imaging and Nanomedicine (C-TRAIN), Cardiovascular Division, Department of Medicine, Washington University School of Medicine, 4320 Forest Park Avenue, Suite 101, Campus Box 8215, St. Louis, MO 63108, USA.
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34
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Roland BP, Kodali R, Mishra R, Wetzel R. A serendipitous survey of prediction algorithms for amyloidogenicity. Biopolymers 2013; 100:780-9. [PMID: 23893755 PMCID: PMC3918212 DOI: 10.1002/bip.22305] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 05/28/2013] [Indexed: 01/16/2023]
Abstract
The 17- amino acid N-terminal segment of the Huntingtin protein, htt(NT), grows into stable α-helix rich oligomeric aggregates when incubated under physiological conditions. We examined 15 scrambled sequence versions of an htt(NT) peptide for their stabilities against aggregation in aqueous solution at low micromolar concentration and physiological conditions. Surprisingly, given their derivation from a sequence that readily assembles into highly stable α-helical aggregates that fail to convert into β-structure, we found that three of these scrambled peptides rapidly grow into amyloid-like fibrils, while two others also develop amyloid somewhat more slowly. The other 10 scrambled peptides do not detectibly form any aggregates after 100 h incubation under these conditions. We then analyzed these sequences using four previously described algorithms for predicting the tendencies of peptides to grow into amyloid or other β-aggregates. We found that these algorithms-Zyggregator, Tango, Waltz, and Zipper-varied greatly in the number of sequences predicted to be amyloidogenic and in their abilities to correctly identify the amyloid forming members of this scrambled peptide collection. The results are discussed in the context of a review of the sequence and structural factors currently thought to be important in determining amyloid formation kinetics and thermodynamics.
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Affiliation(s)
- Bartholomew P Roland
- Department of Structural Biology and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Biomedical Sciences Tower 3, 3501 Fifth Avenue, Pittsburgh, PA, 15260
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35
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Sinnett SE, Sexton JZ, Brenman JE. A High Throughput Assay for Discovery of Small Molecules that Bind AMP-activated Protein Kinase (AMPK). CURRENT CHEMICAL GENOMICS 2013; 7:30-8. [PMID: 24396733 PMCID: PMC3854666 DOI: 10.2174/2213988501307010030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 11/22/2022]
Abstract
AMPK is a conserved heterotrimeric serine-threonine kinase that regulates anabolic and catabolic pathways in eukaryotes. Its central role in cellular and whole body metabolism makes AMPK a commonly proposed therapeutic target for illnesses characterized by abnormal energy regulation, including cancer and diabetes. Many AMPK modulators, however, produce AMPK-independent effects. To identify drugs that modulate AMPK activity independent of the canonical ATP-binding pocket found throughout the kinome, we designed a robust fluorescence-based high throughput screening assay biased toward the identification of molecules that bind the regulatory region of AMPK through displacement of MANT-ADP, a fluorescent ADP analog. Automated pin tools were used to rapidly transfer small molecules to a low volume assay mixture on 384-well plates. Prior to assay validation, we completed a full assay optimization to maximize the signal-to-background and reduce variability for robust detection of small molecules displacing MANT-ADP. After validation, we screened 13,120 molecules and identified 3 positive hits that dose-dependently inhibited the protein-bound signal of MANT-ADP in the presence of both full-length AMPK and the truncated “regulatory fragment” of AMPK, which is missing the kinase active site. The average Z’-factor for the screen was 0.55 and the compound confirmation rate was 60%. Thus, this fluorescence-based assay may be paired with in vitro kinase assays and cell-based assays to help identify molecules that selectively regulate AMPK with fewer off-target effects on other kinases.
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Affiliation(s)
- Sarah E Sinnett
- Neurobiology Curriculum, University of North Carolina Chapel Hill (UNC)
| | - Jonathan Z Sexton
- Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University
| | - Jay E Brenman
- UNC Neuroscience Center; ; Department of Cell Biology and Physiology, UNC
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36
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Ryan BJ, Henehan GT. Overview of approaches to preventing and avoiding proteolysis during expression and purification of proteins. ACTA ACUST UNITED AC 2013; Chapter 5:Unit5.25. [PMID: 23377852 DOI: 10.1002/0471140864.ps0525s71] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteases are enzymes that cleave proteins. They occur widely in nature and play a fundamental role in cellular homeostasis; however, their presence can result in unwanted protein degradation during recombinant protein expression and purification. This unit introduces proteases, specifically focusing on the types commonly encountered during production of recombinant proteins. The strategies used to avoid and to prevent proteolysis are also described, with extensive consideration of the molecular, technical, and logistic methodologies involved.
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Affiliation(s)
- Barry J Ryan
- Food Science and Environmental Health, Dublin Institute of Technology, Dublin, Ireland
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37
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Li R, Li P, Guo X, Jin M, Zhang W, Zhang Q. A Chromatographic Strip for Rapid Semi-quantitative Detection of H5 Subtype Avian Influenza Viruses in Poultry. FOOD ANAL METHOD 2013. [DOI: 10.1007/s12161-013-9606-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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