1
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Qiu Y, Huang T, Cai YD. Review of predicting protein stability changes upon variations. Proteomics 2024; 24:e2300371. [PMID: 38643379 DOI: 10.1002/pmic.202300371] [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: 01/30/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/22/2024]
Abstract
Forecasting alterations in protein stability caused by variations holds immense importance. Improving the thermal stability of proteins is important for biomedical and industrial applications. This review discusses the latest methods for predicting the effects of mutations on protein stability, databases containing protein mutations and thermodynamic parameters, and experimental techniques for efficiently assessing protein stability in high-throughput settings. Various publicly available databases for protein stability prediction are introduced. Furthermore, state-of-the-art computational approaches for anticipating protein stability changes due to variants are reviewed. Each method's types of features, base algorithm, and prediction results are also detailed. Additionally, some experimental approaches for verifying the prediction results of computational methods are introduced. Finally, the review summarizes the progress and challenges of protein stability prediction and discusses potential models for future research directions.
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Affiliation(s)
- Yiling Qiu
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Mathematics and Statistics, Guangdong University of Technology, Guangzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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2
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Mahran R, Vello N, Komulainen A, Malakoutikhah M, Härmä H, Kopra K. Isothermal chemical denaturation assay for monitoring protein stability and inhibitor interactions. Sci Rep 2023; 13:20066. [PMID: 37973851 PMCID: PMC10654576 DOI: 10.1038/s41598-023-46720-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Thermal shift assay (TSA) with altered temperature has been the most widely used method for monitoring protein stability for drug research. However, there is a pressing need for isothermal techniques as alternatives. This urgent demand arises from the limitations of TSA, which can sometimes provide misleading ranking of protein stability and fail to accurately reflect protein stability under physiological conditions. Although differential scanning fluorimetry has significantly improved throughput in comparison to differential scanning calorimetry and differential static light scattering throughput, all these methods exhibit moderate sensitivity. In contrast, current isothermal chemical denaturation (ICD) techniques may not offer the same throughput capabilities as TSA, but it provides more precise information about protein stability and interactions. Unfortunately, ICD also suffers from limited sensitivity, typically in micromolar range. We have developed a novel method to overcome these challenges, namely throughput and sensitivity. The novel Förster Resonance Energy Transfer (FRET)-Probe as an external probe is highly applicable to isothermal protein stability monitoring but also to conventional TSA. We have investigated ICD for multiple proteins with focus on KRASG12C with covalent inhibitors and three chemical denaturants performed at nanomolar protein concentration. Data showed corresponding inhibitor-induced stabilization of KRASG12C to those reported by nucleotide exchange assay.
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Affiliation(s)
- Randa Mahran
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland.
| | - Niklas Vello
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Anita Komulainen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | | | - Harri Härmä
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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3
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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [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] [Indexed: 06/16/2023]
Abstract
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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4
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Kreusser J, Ninni L, Jirasek F, Hasse H. Adsorption of conjugates of lysozyme and fluorescein isothiocyanate in hydrophobic interaction chromatography. J Biotechnol 2022; 360:133-141. [PMID: 36441112 DOI: 10.1016/j.jbiotec.2022.10.015] [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: 09/02/2022] [Revised: 10/10/2022] [Accepted: 10/19/2022] [Indexed: 11/19/2022]
Abstract
Bioconjugates, such as antibody-drug conjugates or fluorescent-labeled proteins, are highly interesting for various applications in medicine and biology. In their production, not only the synthesis is challenging but also the downstream processing, for which hydrophobic interaction chromatography (HIC) is often used. However, in-depth studies of the adsorption of bioconjugates in HIC are still rare. Therefore, in the present work, three different conjugates of lysozyme and fluorescein isothiocyanate (FITC) were synthesized and isolated, and their adsorption on the hydrophobic resin Toyopearl PPG-600 M was systematically studied in batch experiments. The influence of sodium chloride and ammonium sulfate with ionic strengths up to 2000 mM on the adsorption isotherms was investigated at pH 7.0 and 25 °C, and the results were compared to those for pure lysozyme. The conjugation leads to an increase of the adsorption in all studied cases. All studied conjugates contain only a single FITC and differ only in the position of the conjugation on the lysozyme. Despite this, strong differences in the adsorption behavior were observed. Moreover, a mathematical model was developed, which enables the prediction of the adsorption isotherms in the studied systems for varying ionic strengths.
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Affiliation(s)
- Jannette Kreusser
- Laboratory of Engineering Thermodynamics (LTD), TU Kaiserslautern, Kaiserslautern, Germany
| | - Luciana Ninni
- Laboratory of Engineering Thermodynamics (LTD), TU Kaiserslautern, Kaiserslautern, Germany
| | - Fabian Jirasek
- Laboratory of Engineering Thermodynamics (LTD), TU Kaiserslautern, Kaiserslautern, Germany.
| | - Hans Hasse
- Laboratory of Engineering Thermodynamics (LTD), TU Kaiserslautern, Kaiserslautern, Germany
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5
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Assessment of Therapeutic Antibody Developability by Combinations of In Vitro and In Silico Methods. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2313:57-113. [PMID: 34478132 DOI: 10.1007/978-1-0716-1450-1_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although antibodies have become the fastest-growing class of therapeutics on the market, it is still challenging to develop them for therapeutic applications, which often require these molecules to withstand stresses that are not present in vivo. We define developability as the likelihood of an antibody candidate with suitable functionality to be developed into a manufacturable, stable, safe, and effective drug that can be formulated to high concentrations while retaining a long shelf life. The implementation of reliable developability assessments from the early stages of antibody discovery enables flagging and deselection of potentially problematic candidates, while focussing available resources on the development of the most promising ones. Currently, however, thorough developability assessment requires multiple in vitro assays, which makes it labor intensive and time consuming to implement at early stages. Furthermore, accurate in vitro analysis at the early stage is compromised by the high number of potential candidates that are often prepared at low quantities and purity. Recent improvements in the performance of computational predictors of developability potential are beginning to change this scenario. Many computational methods only require the knowledge of the amino acid sequences and can be used to identify possible developability issues or to rank available candidates according to a range of biophysical properties. Here, we describe how the implementation of in silico tools into antibody discovery pipelines is increasingly offering time- and cost-effective alternatives to in vitro experimental screening, thus streamlining the drug development process. We discuss in particular the biophysical and biochemical properties that underpin developability potential and their trade-offs, review various in vitro assays to measure such properties or parameters that are predictive of developability, and give an overview of the growing number of in silico tools available to predict properties important for antibody development, including the CamSol method developed in our laboratory.
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6
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Saikia A, Springer S. Peptide-MHC I complex stability measured by nanoscale differential scanning fluorimetry reveals molecular mechanism of thermal denaturation. Mol Immunol 2021; 136:73-81. [PMID: 34091103 DOI: 10.1016/j.molimm.2021.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/08/2021] [Accepted: 04/29/2021] [Indexed: 12/22/2022]
Abstract
Recombinant major histocompatibility complex class I molecules are used in diagnostic and therapeutic approaches in cancer immunotherapy, with many studies exploring their binding to antigenic peptides. Current techniques for kinetic peptide binding studies are hampered by high sample consumption, low throughput, interference with protein stability, and/or high background signal. Here, we validate nanoscale differential scanning fluorimetry (nanoDSF), a method using the tryptophan fluorescence of class I molecules, for class I/peptide binding, and we use it to determine the molecular mechanism of the thermal denaturation of HLA-A*02:01.
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Affiliation(s)
- Ankur Saikia
- Department of Life Science and Chemistry, Jacobs University Bremen, Germany
| | - Sebastian Springer
- Department of Life Science and Chemistry, Jacobs University Bremen, Germany.
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7
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Atsavapranee B, Stark CD, Sunden F, Thompson S, Fordyce PM. Fundamentals to function: Quantitative and scalable approaches for measuring protein stability. Cell Syst 2021; 12:547-560. [PMID: 34139165 DOI: 10.1016/j.cels.2021.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/16/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022]
Abstract
Folding a linear chain of amino acids into a three-dimensional protein is a complex physical process that ultimately confers an impressive range of diverse functions. Although recent advances have driven significant progress in predicting three-dimensional protein structures from sequence, proteins are not static molecules. Rather, they exist as complex conformational ensembles defined by energy landscapes spanning the space of sequence and conditions. Quantitatively mapping the physical parameters that dictate these landscapes and protein stability is therefore critical to develop models that are capable of predicting how mutations alter function of proteins in disease and informing the design of proteins with desired functions. Here, we review the approaches that are used to quantify protein stability at a variety of scales, from returning multiple thermodynamic and kinetic measurements for a single protein sequence to yielding indirect insights into folding across a vast sequence space. The physical parameters derived from these approaches will provide a foundation for models that extend beyond the structural prediction to capture the complexity of conformational ensembles and, ultimately, their function.
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Affiliation(s)
| | - Catherine D Stark
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Fanny Sunden
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Samuel Thompson
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA.
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8
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Zou B, Zhang L, Xia J, Wang P, Yan Y, Wang X, Adesanya IO. Metal-Organic Frameworks Conjugated Lipase with Enhanced Bio-catalytic Activity and Stability. Appl Biochem Biotechnol 2020; 192:132-145. [DOI: 10.1007/s12010-020-03268-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/13/2020] [Indexed: 10/24/2022]
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9
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Kunz P, Ortale A, Mücke N, Zinner K, Hoheisel JD. Nanobody stability engineering by employing the ΔTm shift; a comparison with apparent rate constants of heat-induced aggregation. Protein Eng Des Sel 2019; 32:241-249. [PMID: 31340035 DOI: 10.1093/protein/gzz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 06/09/2019] [Accepted: 06/29/2019] [Indexed: 12/30/2022] Open
Abstract
The antigen-binding domains of camelid heavy-chain antibodies, also called nanobodies, gained strong attention because of their unique functional and biophysical properties. They gave rise to an entire spectrum of applications in biotechnology, research and medicine. Despite several reports about reversibly refolding nanobodies, protein aggregation plays a major role in nanobody thermoresistance, asking for strategies to engineer their refolding behavior. Here, we use measurements of nanobody aggregation kinetics to validate structural features in the nanobody fold that are suppressing heat-induced nanobody aggregation. Furthermore, the kinetic measurements yielded a detailed insight into the concept of the ΔTm shift, a metric for protein aggregation propensities obtained from differential scanning fluorimetry measurements. By relating the equilibrium measurements of the ΔTm shift to the kinetic measurements of heat-induced nanobody aggregation, a distinct relationship could be identified that allows a prediction of nanobody aggregation rates from a simple equilibrium measurement of ΔTm.
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Affiliation(s)
- Patrick Kunz
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
| | - Aurelio Ortale
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
| | - Norbert Mücke
- Division of Biophysics of Macromolecules, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
| | - Katinka Zinner
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
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10
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Moore-Kelly C, Welsh J, Rodger A, Dafforn TR, Thomas ORT. Automated High-Throughput Capillary Circular Dichroism and Intrinsic Fluorescence Spectroscopy for Rapid Determination of Protein Structure. Anal Chem 2019; 91:13794-13802. [PMID: 31584804 PMCID: PMC7006967 DOI: 10.1021/acs.analchem.9b03259] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
Assessing
the physical stability of proteins is one of the most
important challenges in the development, manufacture, and formulation
of biotherapeutics. Here, we describe a method for combining and automating
circular dichroism and intrinsic protein fluorescence spectroscopy.
By robotically injecting samples from a 96-well plate into an optically
compliant capillary flow cell, complementary information about the
secondary and tertiary structural state of a protein can be collected
in an unattended manner from considerably reduced volumes of sample
compared to conventional techniques. We demonstrate the accuracy and
reproducibility of this method. Furthermore, we show how structural
screening can be used to monitor unfolding of proteins in two case
studies using (i) a chaotropic denaturant (urea) and (ii) low-pH buffers
used for monoclonal antibody (mAb) purification during Protein A chromatography.
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Affiliation(s)
| | - John Welsh
- Pall Biotech , Southampton Road , Portsmouth , PO6 4BQ , U.K
| | - Alison Rodger
- Department of Molecular Sciences , Macquarie University , Macquarie Park , Sydney , New South Wales 2109 , Australia
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11
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The role of circular dichroism spectroscopy in the era of integrative structural biology. Curr Opin Struct Biol 2019; 58:191-196. [DOI: 10.1016/j.sbi.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 12/25/2022]
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12
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Jiang B, Jain A, Lu Y, Hoag SW. Probing Thermal Stability of Proteins with Temperature Scanning Viscometer. Mol Pharm 2019; 16:3687-3693. [DOI: 10.1021/acs.molpharmaceut.9b00598] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bowen Jiang
- Department of Pharmaceutical Sciences, University of Maryland, 20 North Pine Street, Baltimore, Maryland 21201, United States
| | - Amita Jain
- Department of Pharmaceutical Sciences, University of Maryland, 20 North Pine Street, Baltimore, Maryland 21201, United States
| | - Yuwei Lu
- Department of Pharmaceutical Sciences, University of Maryland, 20 North Pine Street, Baltimore, Maryland 21201, United States
| | - Stephen W. Hoag
- Department of Pharmaceutical Sciences, University of Maryland, 20 North Pine Street, Baltimore, Maryland 21201, United States
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Tadepalli S, Wang Z, Slocik J, Naik RR, Singamaneni S. Effect of size and curvature on the enzyme activity of bionanoconjugates. NANOSCALE 2017; 9:15666-15672. [PMID: 28993826 DOI: 10.1039/c7nr02434g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biotic-abiotic hybrids comprised of globular proteins and functional nanostructures with complementary and synergistic properties are central to a number of bionanotechnological applications. A comprehensive understanding of the effect of physicochemical properties of abiotic nanostructures on the biological activity of the bionanoconjugates is critical in the design of these bio-nano hybrids. In this study, using size and curvature-controlled gold nanoparticles as a model abiotic system, we investigated the effect of hydrodynamic diameter and surface curvature on the activity of a model enzyme, horseradish peroxidase (HRP), adsorbed on the surface of the nanostructures. In contrast with the previous studies, we have employed a novel class of gold superstructures (gold nanoparticles on spheres) to deconvolute the effects of size and curvature on the catalytic activity of the bionanoconjugates. This study improves our understanding of the bio/nano interface and the design of bioinorganic hybrids with potential applications in biomimetic and bioenabled sensors, energy harvesting, optoelectronic components and devices, responsive and autonomous materials.
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Affiliation(s)
- Sirimuvva Tadepalli
- Institute of Material Science and Engineering and Department of Mechanical Engineering and Material Science, Washington University in St Louis, St Louis, MO 63130, USA.
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14
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Tadepalli S, Wang Z, Liu KK, Jiang Q, Slocik J, Naik RR, Singamaneni S. Influence of Surface Charge of the Nanostructures on the Biocatalytic Activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6611-6619. [PMID: 28605903 DOI: 10.1021/acs.langmuir.6b04490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The physicochemical properties of abiotic nanostructures determine the structure and function of biological counterparts in biotic-abiotic nanohybrids. A comprehensive understanding of the interfacial interactions and the predictive capability of their structure and function is paramount for virtually all fields of bionanotechnology. In this study, using plasmonic nanostructures as a model abiotic system, we investigate the effect of the surface charge of nanostructures on the biocatalytic reaction kinetics of a bound enzyme. We found that the surface charge of nanostructures profoundly influences the structure, orientation, and activity of the bound enzyme. Furthermore, the interactions of the enzyme with nanoparticles result in stable conjugates that retain their functionality at elevated temperatures, unlike their free counterparts that lose their secondary structure and biocatalytic activity.
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Affiliation(s)
- Sirimuvva Tadepalli
- Institute of Material Science and Engineering and Department of Mechanical Engineering and Material Science, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Zheyu Wang
- Institute of Material Science and Engineering and Department of Mechanical Engineering and Material Science, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Keng-Ku Liu
- Institute of Material Science and Engineering and Department of Mechanical Engineering and Material Science, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Qisheng Jiang
- Institute of Material Science and Engineering and Department of Mechanical Engineering and Material Science, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Joseph Slocik
- 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Rajesh R Naik
- 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Srikanth Singamaneni
- Institute of Material Science and Engineering and Department of Mechanical Engineering and Material Science, Washington University in St. Louis , St. Louis, Missouri 63130, United States
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15
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Abstract
BACKGROUND Variable domains of camelid heavy-chain antibodies, commonly named nanobodies, have high biotechnological potential. In view of their broad range of applications in research, diagnostics and therapy, engineering their stability is of particular interest. One important aspect is the improvement of thermostability, because it can have immediate effects on conformational stability, protease resistance and aggregation propensity of the protein. METHODS We analyzed the sequences and thermostabilities of 78 purified nanobody binders. From this data, potentially stabilizing amino acid variations were identified and studied experimentally. RESULTS Some mutations improved the stability of nanobodies by up to 6.1°C, with an average of 2.3°C across eight modified nanobodies. The stabilizing mechanism involves an improvement of both conformational stability and aggregation behavior, explaining the variable degree of stabilization in individual molecules. In some instances, variations predicted to be stabilizing actually led to thermal destabilization of the proteins. The reasons for this contradiction between prediction and experiment were investigated. CONCLUSIONS The results reveal a mutational strategy to improve the biophysical behavior of nanobody binders and indicate a species-specificity of nanobody architecture. GENERAL SIGNIFICANCE This study illustrates the potential and limitations of engineering nanobody thermostability by merging sequence information with stability data, an aspect that is becoming increasingly important with the recent development of high-throughput biophysical methods.
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16
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Krainer G, Gracia P, Frotscher E, Hartmann A, Gröger P, Keller S, Schlierf M. Slow Interconversion in a Heterogeneous Unfolded-State Ensemble of Outer-Membrane Phospholipase A. Biophys J 2017. [PMID: 28629619 DOI: 10.1016/j.bpj.2017.05.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Structural and dynamic investigations of unfolded proteins are important for understanding protein-folding mechanisms as well as the interactions of unfolded polypeptide chains with other cell components. In the case of outer-membrane proteins (OMPs), unfolded-state properties are of particular physiological relevance, because these proteins remain unfolded for extended periods of time during their biogenesis and rely on interactions with binding partners to support proper folding. Using a combination of ensemble and single-molecule spectroscopy, we have scrutinized the unfolded state of outer-membrane phospholipase A (OmpLA) to provide a detailed view of its structural dynamics on timescales from nanoseconds to milliseconds. We find that even under strongly denaturing conditions and in the absence of residual secondary structure, OmpLA populates an ensemble of slowly (>100 ms) interconverting and conformationally heterogeneous unfolded states that lack the fast chain-reconfiguration motions expected for an unstructured, fully unfolded chain. The drastically slowed sampling of potentially folding-competent states, as compared with a random-coil polypeptide, may contribute to the slow in vitro folding kinetics observed for many OMPs. In vivo, however, slow intramolecular long-range dynamics might be advantageous for entropically favored binding of unfolded OMPs to chaperones and, by facilitating conformational selection after release from chaperones, for preserving binding-competent conformations before insertion into the outer membrane.
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Affiliation(s)
- Georg Krainer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany; Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Pablo Gracia
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Erik Frotscher
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Andreas Hartmann
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Philip Gröger
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany.
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany.
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17
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Jelińska A, Zagożdżon A, Górecki M, Wisniewska A, Frelek J, Holyst R. Denaturation of proteins by surfactants studied by the Taylor dispersion analysis. PLoS One 2017; 12:e0175838. [PMID: 28426809 PMCID: PMC5398553 DOI: 10.1371/journal.pone.0175838] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/01/2017] [Indexed: 11/29/2022] Open
Abstract
We showed that the Taylor Dispersion Analysis (TDA) is a fast and easy to use method for the study of denaturation proteins. We applied TDA to study denaturation of β-lactoglobulin, transferrin, and human insulin by anionic surfactant sodium dodecyl sulfate (SDS). A series of measurements at constant protein concentration (for transferrin was 1.9 x 10−5 M, for β- lactoglobulin was 7.6 x 10−5 M, and for insulin was 1.2 x 10−4 M) and varying SDS concentrations were carried out in the phosphate-buffered saline (PBS). The structural changes were analyzed based on the diffusion coefficients of the complexes formed at various surfactant concentrations. The concentration of surfactant was varied in the range from 1.2 x 10−4 M to 8.7 x 10−2 M. We determined the minimum concentration of the surfactant necessary to change the native conformation of the proteins. The minimal concentration of SDS for β-lactoglobulin and transferrin was 4.3 x 10−4 M and for insulin 2.3 x 10−4 M. To evaluate the TDA as a novel method for studying denaturation of proteins we also applied other methods i.e. electronic circular dichroism (ECD) and dynamic light scattering (DLS) to study the same phenomenon. The results obtained using these methods were in agreement with the results from TDA.
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Affiliation(s)
- Aldona Jelińska
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Zagożdżon
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | | | - Jadwiga Frelek
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
- * E-mail:
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18
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Oluwole AO, Danielczak B, Meister A, Babalola JO, Vargas C, Keller S. Solubilization of Membrane Proteins into Functional Lipid-Bilayer Nanodiscs Using a Diisobutylene/Maleic Acid Copolymer. Angew Chem Int Ed Engl 2017; 56:1919-1924. [PMID: 28079955 PMCID: PMC5299484 DOI: 10.1002/anie.201610778] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/24/2016] [Indexed: 12/22/2022]
Abstract
Once removed from their natural environment, membrane proteins depend on membrane-mimetic systems to retain their native structures and functions. To this end, lipid-bilayer nanodiscs that are bounded by scaffold proteins or amphiphilic polymers such as styrene/maleic acid (SMA) copolymers have been introduced as alternatives to detergent micelles and liposomes for in vitro membrane-protein research. Herein, we show that an alternating diisobutylene/maleic acid (DIBMA) copolymer shows equal performance to SMA in solubilizing phospholipids, stabilizes an integral membrane enzyme in functional bilayer nanodiscs, and extracts proteins of various sizes directly from cellular membranes. Unlike aromatic SMA, aliphatic DIBMA has only a mild effect on lipid acyl-chain order, does not interfere with optical spectroscopy in the far-UV range, and does not precipitate in the presence of low millimolar concentrations of divalent cations.
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Affiliation(s)
- Abraham Olusegun Oluwole
- Molecular BiophysicsUniversity of KaiserslauternErwin-Schrödinger-Str. 1367663KaiserslauternGermany
- Department of ChemistryUniversity of Ibadan200284IbadanNigeria
| | - Bartholomäus Danielczak
- Molecular BiophysicsUniversity of KaiserslauternErwin-Schrödinger-Str. 1367663KaiserslauternGermany
| | - Annette Meister
- Institute of Chemistry and Institute of Biochemistry and BiotechnologyMartin Luther University Halle-WittenbergVon-Danckelmann-Platz 406120HalleGermany
| | | | - Carolyn Vargas
- Molecular BiophysicsUniversity of KaiserslauternErwin-Schrödinger-Str. 1367663KaiserslauternGermany
| | - Sandro Keller
- Molecular BiophysicsUniversity of KaiserslauternErwin-Schrödinger-Str. 1367663KaiserslauternGermany
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19
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Oluwole AO, Danielczak B, Meister A, Babalola JO, Vargas C, Keller S. Solubilisierung von Membranproteinen in funktionelle Lipiddoppelschicht-Nanodiscs mithilfe eines Diisobutylen/ Maleinsäure-Copolymers. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Abraham Olusegun Oluwole
- Molekulare Biophysik; Technische Universität Kaiserslautern; Erwin-Schrödinger-Str. 13 67663 Kaiserslautern Deutschland
- Department of Chemistry; University of Ibadan; 200284 Ibadan Nigeria
| | - Bartholomäus Danielczak
- Molekulare Biophysik; Technische Universität Kaiserslautern; Erwin-Schrödinger-Str. 13 67663 Kaiserslautern Deutschland
| | - Annette Meister
- Institut für Chemie und Institut für Biochemie und Biotechnologie; Martin-Luther-Universität Halle-Wittenberg; Von-Danckelmann-Platz 4 06120 Halle Deutschland
| | | | - Carolyn Vargas
- Molekulare Biophysik; Technische Universität Kaiserslautern; Erwin-Schrödinger-Str. 13 67663 Kaiserslautern Deutschland
| | - Sandro Keller
- Molekulare Biophysik; Technische Universität Kaiserslautern; Erwin-Schrödinger-Str. 13 67663 Kaiserslautern Deutschland
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20
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Hussain R, Jávorfi T, Rudd TR, Siligardi G. High-throughput SRCD using multi-well plates and its applications. Sci Rep 2016; 6:38028. [PMID: 28004702 PMCID: PMC5177961 DOI: 10.1038/srep38028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 11/03/2016] [Indexed: 12/03/2022] Open
Abstract
The sample compartment for high-throughput synchrotron radiation circular dichroism (HT-SRCD) has been developed to satisfy an increased demand of protein characterisation in terms of folding and binding interaction properties not only in the traditional field of structural biology but also in the growing research area of material science with the potential to save time by 80%. As the understanding of protein behaviour in different solvent environments has increased dramatically the development of novel functions such as recombinant proteins modified to have different functions from harvesting solar energy to metabolonics for cleaning heavy and metal and organic molecule pollutions, there is a need to characterise speedily these system.
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Affiliation(s)
- Rohanah Hussain
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
| | - Tamás Jávorfi
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
| | - Timothy R Rudd
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
| | - Giuliano Siligardi
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
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21
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Panigrahi R, Arutyunova E, Panwar P, Gimpl K, Keller S, Lemieux MJ. Reversible Unfolding of Rhomboid Intramembrane Proteases. Biophys J 2016; 110:1379-90. [PMID: 27028647 DOI: 10.1016/j.bpj.2016.01.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 12/20/2022] Open
Abstract
Denaturant-induced unfolding of helical membrane proteins provides insights into their mechanism of folding and domain organization, which take place in the chemically heterogeneous, anisotropic environment of a lipid membrane. Rhomboid proteases are intramembrane proteases that play key roles in various diseases. Crystal structures have revealed a compact helical bundle with a buried active site, which requires conformational changes for the cleavage of transmembrane substrates. A dimeric form of the rhomboid protease has been shown to be important for activity. In this study, we examine the mechanism of refolding for two distinct rhomboids to gain insight into their secondary structure-activity relationships. Although helicity is largely abolished in the unfolded states of both proteins, unfolding is completely reversible for HiGlpG but only partially reversible for PsAarA. Refolding of both proteins results in reassociation of the dimer, with a 90% regain of catalytic activity for HiGlpG but only a 70% regain for PsAarA. For both proteins, a broad, gradual transition from the native, folded state to the denatured, partly unfolded state was revealed with the aid of circular dichroism spectroscopy as a function of denaturant concentration, thus arguing against a classical two-state model as found for many globular soluble proteins. Thermal denaturation has irreversible destabilizing effects on both proteins, yet reveals important functional details regarding substrate accessibility to the buried active site. This concerted biophysical and functional analysis demonstrates that HiGlpG, with a simple six-transmembrane-segment organization, is more robust than PsAarA, which has seven predicted transmembrane segments, thus rendering HiGlpG amenable to in vitro studies of membrane-protein folding.
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Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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22
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Phan QH, Lo YL, Huang CL. Surface plasmon resonance prism coupler for enhanced circular dichroism sensing. OPTICS EXPRESS 2016; 24:12812-12824. [PMID: 27410300 DOI: 10.1364/oe.24.012812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel method for enhanced circular dichroism (CD) detection is proposed based on a surface plasmon resonance (SPR) prism coupler and a polarization scanning ellipsometry technique. An analytical model is derived to extract the CD and degree of polarization (DOP) properties of optical samples with and without scattering effects, respectively. The validity of the analytical model is confirmed by means of numerical simulations. The simulation results show that the proposed detection method has a sensitivity of 10-5~10-6 RIU (refractive index unit) for refractive indices in the range of 1.32~1.36 and 1.3100~1.3118. The practical feasibility of the proposed method is demonstrated by the experimental results for the sensitivity of the CD with the chlorophyllin samples with/without scattering effect. It is shown that for both types of sample, the extracted CD value increases linearly with the chlorophyll concentration over the considered range. In general, the results obtained in this study show that the measured CD response is highly sensitive to the polarization scanning angle. Consequently, the potential of polarization scanning ellipsometry for high-resolution CD detection is confirmed.
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23
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Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide-MHC complexes. J Immunol Methods 2016; 432:95-101. [PMID: 26906089 DOI: 10.1016/j.jim.2016.02.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/17/2016] [Accepted: 02/17/2016] [Indexed: 11/20/2022]
Abstract
Measurements of thermal stability by circular dichroism (CD) spectroscopy have been widely used to assess the binding of peptides to MHC proteins, particularly within the structural immunology community. Although thermal stability assays offer advantages over other approaches such as IC50 measurements, CD-based stability measurements are hindered by large sample requirements and low throughput. Here we demonstrate that an alternative approach based on differential scanning fluorimetry (DSF) yields results comparable to those based on CD for both class I and class II complexes. As they require much less sample, DSF-based measurements reduce demands on protein production strategies and are amenable for high throughput studies. DSF can thus not only replace CD as a means to assess peptide/MHC thermal stability, but can complement other peptide-MHC binding assays used in screening, epitope discovery, and vaccine design. Due to the physical process probed, DSF can also uncover complexities not observed with other techniques. Lastly, we show that DSF can also be used to assess peptide/MHC kinetic stability, allowing for a single experimental setup to probe both binding equilibria and kinetics.
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24
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Continuous polyethylene glycol precipitation of recombinant antibodies: Sequential precipitation and resolubilization. Process Biochem 2016. [DOI: 10.1016/j.procbio.2015.11.032] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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25
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Deng S, Zhang T, Ji X, Wan Y, Xin P, Shan D, Zhang X. Detection of zinc finger protein (EGR1) based on electrogenerated chemiluminescence from singlet oxygen produced in a nanoclay-supported porphyrin environment. Anal Chem 2015; 87:9155-62. [PMID: 26301820 DOI: 10.1021/acs.analchem.5b01318] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early growth response protein 1 (EGR1), as a characteristic example of zinc finger proteins, acts as a transcription factor in eukaryotic cells, mediating protein-protein interactions. Here, a novel electrochemiluminescence (ECL)-based protocol for EGR1 assay was developed with a new eco-friendly emitter: singlet oxygen produced in the vicinity of nanoclay-supported zinc proto-porphyrin IX (ZnPPIX). Its electrochemical reduction stimulates an intense monochromic CL irradiation at 644 nm from the dissolved oxygen as endogenous coreactant in the aqueous solution. This ECL derivation was rationalized via hyphenated spectroscopy and theoretical calculation. To promote hydrophilicity and solid-state immobilization of porphyrins, the lamellar artificial laponite was employed as a nanocarrier owning to its large specific area without the blackbody effect. The facile exfoliation of laponite produced quality monolayered nanosheets and facilitated the adsorption and flattening of PPIX upon the surface, resulting in a highly efficient ECL emission. Based on the release of Zn(2+) in zinc finger domains of EGR1 upon contact with the ECL-inactive PPIX, which was monitored by circular dichroism and UV-absorption, a sensitive Zn(2+)-selective electrode for the "signal-on" detection of EGR1 was prepared with a detection limit down to 0.48 pg mL(-1) and a linearity over 6 orders of magnitude. The proposed porphyrin-based ECL system thus infused fresh blood into the traditional ECL family, showing great promise in bioassays of structural Zn(II) proteins and zinc finger-binding nucleotides.
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Affiliation(s)
- Shengyuan Deng
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Tingting Zhang
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Xubo Ji
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Ying Wan
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China.,Intelligent Microsystem Technology and Engineering Center, School of Mechanical Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Peng Xin
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Dan Shan
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Xueji Zhang
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
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26
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Li S, Peng Z, Leblanc RM. Method To Determine Protein Concentration in the Protein-Nanoparticle Conjugates Aqueous Solution Using Circular Dichroism Spectroscopy. Anal Chem 2015; 87:6455-9. [PMID: 26070096 DOI: 10.1021/acs.analchem.5b01451] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Considerable efforts have been made to synthesize and characterize protein-nanoparticle conjugates (protein-NPs) for their promising applications in bionanotechnology. However, protein concentration determination in the protein-NPs has so far not been reported. In this Letter, we present a simple and nondestructive approach to quantify the protein concentration in the protein-NPs aqueous solution using circular dichroism (CD) spectroscopy. Carbon dots (∼4 nm), gold nanoparticles (∼10 nm), and polyethylene glycol (PEG, molecular weight ∼3000) were either physically mixed or covalently conjugated (not in the case of gold nanoparticles) with proteins (human transferrin, human serum albumin, and ovalbumin). We were able to quantify the protein concentration in the protein-nanoparticle conjugates using a calibration curve from the CD spectra.
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Affiliation(s)
- Shanghao Li
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Zhili Peng
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Roger M Leblanc
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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27
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Siligardi G, Hussain R. CD spectroscopy: an essential tool for quality control of protein folding. Methods Mol Biol 2015; 1261:255-76. [PMID: 25502204 DOI: 10.1007/978-1-4939-2230-7_14] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The production of diffraction quality protein crystals for X-ray crystallography has been greatly accelerated by the development of high-throughput protein (HTP) methods, which enable a large number of crystallization conditions to be rapidly investigated. Monitoring sample quality and the effect of crystallization buffers on protein behavior in solution should be considered as part of the crystallization experiment. Circular Dichroism (CD) spectroscopy is the ideal technique for these tasks as it can be operated in a high-throughput mode. Using CD to screen ligand binding interactions could show whether protein function/activity is retained, altered, or lost under different crystallization conditions. In this chapter, several methods for high-throughput CD (HTCD) applied to the preparation of proteins for crystallization will be presented. Quality control (QC) of protein batches in terms of conformational folding is often disregarded in protein production. Examples of batch-to-batch variation in the local tertiary structure of aromatic side chain residues revealed by CD will be discussed. In some of the examples, the fact that ligand binding properties were affected by changes in folding clearly shows that the characterization of folding of recombinant protein batches should not be ignored but be implemented as an important part of protein quality control.
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Affiliation(s)
- Giuliano Siligardi
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Fermi Ave, Didcot, Chilton, Oxfordshire, OX11 0DE, UK,
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28
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Broecker J, Fiedler S, Gimpl K, Keller S. Polar Interactions Trump Hydrophobicity in Stabilizing the Self-Inserting Membrane Protein Mistic. J Am Chem Soc 2014; 136:13761-8. [DOI: 10.1021/ja5064795] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jana Broecker
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Sebastian Fiedler
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Katharina Gimpl
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straβe 13, 67663 Kaiserslautern, Germany
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29
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Jacso T, Bardiaux B, Broecker J, Fiedler S, Baerwinkel T, Mainz A, Fink U, Vargas C, Oschkinat H, Keller S, Reif B. The Mechanism of Denaturation and the Unfolded State of the α-Helical Membrane-Associated Protein Mistic. J Am Chem Soc 2013; 135:18884-91. [DOI: 10.1021/ja408644f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Tomas Jacso
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Helmholtz-Zentrum
München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Benjamin Bardiaux
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Jana Broecker
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Sebastian Fiedler
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Tom Baerwinkel
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Helmholtz-Zentrum
München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Andi Mainz
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Uwe Fink
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Carolyn Vargas
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Hartmut Oschkinat
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Sandro Keller
- Molecular
Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Straße
13, 67663 Kaiserslautern, Germany
| | - Bernd Reif
- Center
for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
- Helmholtz-Zentrum
München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
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30
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Siligardi G, Hussain R, Patching SG, Phillips-Jones MK. Ligand- and drug-binding studies of membrane proteins revealed through circular dichroism spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:34-42. [PMID: 23811229 DOI: 10.1016/j.bbamem.2013.06.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/13/2013] [Accepted: 06/14/2013] [Indexed: 11/15/2022]
Abstract
A great number of membrane proteins have proven difficult to crystallise for use in X-ray crystallographic structural determination or too complex for NMR structural studies. Circular dichroism (CD) is a fast and relatively easy spectroscopic technique to study protein conformational behaviour. In this review examples of the applications of CD and synchrotron radiation CD (SRCD) to membrane protein ligand binding interaction studies are discussed. The availability of SRCD has been an important advancement in recent progress, most particularly because it can be used to extend the spectral region in the far-UV region (important for increasing the accuracy of secondary structure estimations) and for working with membrane proteins available in only small quantities for which SRCD has facilitated molecular recognition studies. Such studies have been accomplished by probing in the near-UV region the local tertiary structure of aromatic amino acid residues upon addition of chiral or non-chiral ligands using long pathlength cells of small volume capacity. In particular, this review describes the most recent use of the technique in the following areas: to obtain quantitative data on ligand binding (exemplified by the FsrC membrane sensor kinase receptor); to distinguish between functionally similar drugs that exhibit different mechanisms of action towards membrane proteins (exemplified by secretory phospholipase A2); and to identify suitable detergent conditions to observe membrane protein-ligand interactions using stabilised proteins (exemplified by the antiseptic transporter SugE). Finally, the importance of characterising in solution the conformational behaviour and ligand binding properties of proteins in both far- and near-UV regions is discussed. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.
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Affiliation(s)
- Giuliano Siligardi
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK; School of Biological Sciences, University of Liverpool, Liverpool, UK.
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