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Vishwakarma P, Puri S, Banerjee M, Chang CY, Chang CC, Chaudhuri TK. Deciphering the Thermal Stability of Bacteriophage MS2-Derived Virus-like Particle and Its Engineered Variant. ACS Biomater Sci Eng 2024; 10:4812-4822. [PMID: 38976823 DOI: 10.1021/acsbiomaterials.4c00770] [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: 07/10/2024]
Abstract
RNA bacteriophage MS2-derived virus-like particles (VLPs) have been widely used in biomedical research as model systems to study virus assembly, structure-function relationships, vaccine development, and drug delivery. Considering the diverse utility of these VLPs, a systemic engineering approach has been utilized to generate smaller particles with optimal serum stability and tissue penetrance. Additionally, it is crucial to demonstrate the overall stability of these mini MS2 VLPs, ensuring cargo protection until they reach their target cell/organ. However, no detailed analysis of the thermal stability and heat-induced disassembly of MS2 VLPs has yet been attempted. In this work, we investigated the thermal stability of both wild-type (WT) MS2 VLP and its "mini" variant containing S37P mutation (mini MS2 VLP). The mini MS2 VLP exhibits a higher capsid melting temperature (Tm) when compared to its WT MS2 VLP counterpart, possibly attributed to its smaller interdimer angle. Our study presents that the thermal unfolding of MS2 VLPs follows a sequential process involving particle destabilization, nucleic acid exposure/melting, and disassembly of VLP. This observation underscores the disruption of cooperative intersubunit interactions and protein-nucleic acid interactions, shedding light on the mechanism of heat-induced VLP disassembly.
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Affiliation(s)
- Pragati Vishwakarma
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Sarita Puri
- Department of Bioscience, University of Milan, Milan 20133, Italy
| | - Manidipa Banerjee
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Chia-Yu Chang
- Department of Biological Sciences and Technology, National Yang-Ming Chiao Tsung University, Hsinchu 30068, Taiwan
| | - Chia-Ching Chang
- Department of Biological Sciences and Technology, National Yang-Ming Chiao Tsung University, Hsinchu 30068, Taiwan
- Department of Electrophysics, National Yang-Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang-Ming Chiao Tung University, Hsinchu 30068, Taiwan
- International College of Semiconductor Technology, National Yang-Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Tapan K Chaudhuri
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi 110016, India
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Wongnak R, Brindha S, Oba M, Yoshizue T, Islam MD, Islam MM, Takemae H, Mizutani T, Kuroda Y. Non-Glycosylated SARS-CoV-2 Omicron BA.5 Receptor Binding Domain (RBD) with a Native-like Conformation Induces a Robust Immune Response with Potent Neutralization in a Mouse Model. Molecules 2024; 29:2676. [PMID: 38893549 PMCID: PMC11173568 DOI: 10.3390/molecules29112676] [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: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
The Omicron BA.5 variant of SARS-CoV-2 is known for its high transmissibility and its capacity to evade immunity provided by vaccine protection against the (original) Wuhan strain. In our prior research, we successfully produced the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein in an E. coli expression system. Extensive biophysical characterization indicated that, even without glycosylation, the RBD maintained native-like conformational and biophysical properties. The current study explores the immunogenicity and neutralization capacity of the E. coli-expressed Omicron BA.5 RBD using a mouse model. Administration of three doses of the RBD without any adjuvant elicited high titer antisera of up to 7.3 × 105 and up to 1.6 × 106 after a booster shot. Immunization with RBD notably enhanced the population of CD44+CD62L+ T cells, indicating the generation of T cell memory. The in vitro assays demonstrated the antisera's protective efficacy through significant inhibition of the interaction between SARS-CoV-2 and its human receptor, ACE2, and through potent neutralization of a pseudovirus. These findings underscore the potential of our E. coli-expressed RBD as a viable vaccine candidate against the Omicron variant of SARS-CoV-2.
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Affiliation(s)
- Rawiwan Wongnak
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
| | - Subbaian Brindha
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
| | - Mami Oba
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Takahiro Yoshizue
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
| | - Md. Din Islam
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
| | - M. Monirul Islam
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Hitoshi Takemae
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Tetsuya Mizutani
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu-shi 183-8509, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Nakamachi 2-24-16, Tokyo 184-8588, Japan; (R.W.); (S.B.); (T.Y.); (M.D.I.)
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan; (M.O.); (H.T.); (T.M.)
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3
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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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Jennings CC, Freidenberger M, Christensen SA, Conlin J, Freidenberger O, Kenealey JD. Thermal characterization and separation of whey proteins by differential scanning calorimetry. Food Chem 2024; 441:138347. [PMID: 38183724 DOI: 10.1016/j.foodchem.2023.138347] [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: 10/09/2023] [Revised: 12/16/2023] [Accepted: 12/30/2023] [Indexed: 01/08/2024]
Abstract
Most commercially available whey products contain a mixture of 6-7 whey proteins; however, there is an increased focus on using the individual whey proteins for their unique biological activities. Before extracting individual whey proteins for use, it is important to quantify how much of a particular protein is present in whey mixtures as well as if the protein is still structurally folded. We first characterized the denaturation temperature and enthalpy values for the six purified whey proteins at six pHs (3-9) and under ion chelation using a nano-differential scanning calorimeter (DSC). From the individual protein scans, we determined the optimal condition for detecting all 6 proteins on a single DSC scan was whey in an EDTA MOPs pH 6.7 buffer.
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Affiliation(s)
- Charity C Jennings
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, UT 84606, United States
| | - McCall Freidenberger
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, UT 84606, United States
| | - Shawn A Christensen
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, UT 84606, United States
| | - Joy Conlin
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, UT 84606, United States
| | - Olivia Freidenberger
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, UT 84606, United States
| | - Jason D Kenealey
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, UT 84606, United States.
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Carvalho SF, Custódio MH, Pereiro AB, Araújo JMM. Towards Enhanced Tunability of Aqueous Biphasic Systems: Furthering the Grasp of Fluorinated Ionic Liquids in the Purification of Proteins. Int J Mol Sci 2024; 25:5766. [PMID: 38891953 PMCID: PMC11172314 DOI: 10.3390/ijms25115766] [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: 04/12/2024] [Revised: 05/11/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
This work unfolds functionalized ABSs composed of FILs ([C2C1Im][C4F9SO3] and [N1112(OH)][C4F9SO3]), mere fluoro-containing ILs ([C2C1Im][CF3SO3] and [C4C1Im][CF3SO3]), known globular protein stabilizers (sucrose and [N1112(OH)][C4F9SO3]), low-molecular-weight carbohydrate (glucose), and even high-charge density salt (K3PO4). The ternary phase diagrams were determined, stressing that FILs highly increased the ability for ABS formation. The functionalized ABSs (FILs vs. mere fluoro-containing ILs) were used to extract lysozyme (Lys). The ABSs' biphasic regions were screened in terms of protein biocompatibility, analyzing the impact of ABS phase-forming components in Lys by UV-VIS spectrophotometry, CD spectroscopy, fluorescence spectroscopy, DSC, and enzyme assay. Lys partition behavior was characterized in terms of extraction efficiency (% EE). The structure, stability, and function of Lys were maintained or improved throughout the extraction step, as evaluated by CD spectroscopy, DSC, enzyme assay, and SDS-PAGE. Overall, FIL-based ABSs are more versatile and amenable to being tuned by the adequate choice of the phase-forming components and selecting the enriched phase. Binding studies between Lys and ABS phase-forming components were attained by MST, demonstrating the strong interaction between Lys and FILs aggregates. Two of the FIL-based ABSs (30 %wt [C2C1Im][C4F9SO3] + 2 %wt K3PO4 and 30 %wt [C2C1Im][C4F9SO3] + 25 %wt sucrose) allowed the simultaneous purification of Lys and BSA in a single ABS extraction step with high yield (extraction efficiency up to 100%) for both proteins. The purity of both recovered proteins was validated by SDS-PAGE analysis. Even with a high-charge density salt, the FIL-based ABSs developed in this work seem more amenable to be tuned. Lys and BSA were purified through selective partition to opposite phases in a single FIL-based ABS extraction step. FIL-based ABSs are proposed as an improved extraction step for proteins, based on their biocompatibility, customizable properties, and selectivity.
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Affiliation(s)
| | | | | | - João M. M. Araújo
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal; (S.F.C.); (M.H.C.); (A.B.P.)
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6
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Zambrano P, Manrique-Moreno M, Petit K, Colina JR, Jemiola-Rzeminska M, Suwalsky M, Strzalka K. Differential scanning calorimetry in drug-membrane interactions. Biochem Biophys Res Commun 2024; 709:149806. [PMID: 38579619 DOI: 10.1016/j.bbrc.2024.149806] [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: 09/22/2023] [Revised: 03/04/2024] [Accepted: 03/18/2024] [Indexed: 04/07/2024]
Abstract
Differential Scanning Calorimetry (DSC) is a central technique in investigating drug - membrane interactions, a critical component of pharmaceutical research. DSC measures the heat difference between a sample of interest and a reference as a function of temperature or time, contributing essential knowledge on the thermally induced phase changes in lipid membranes and how these changes are affected by incorporating pharmacological substances. The manuscript discusses the use of phospholipid bilayers, which can form structures like unilamellar and multilamellar vesicles, providing a simplified yet representative membrane model to investigate the complex dynamics of how drugs interact with and penetrate cellular barriers. The manuscript consolidates data from various studies, providing a comprehensive understanding of the mechanisms underlying drug - membrane interactions, the determinants that influence these interactions, and the crucial role of DSC in elucidating these components. It further explores the interactions of specific classes of drugs with phospholipid membranes, including non-steroidal anti-inflammatory drugs, anticancer agents, natural products with antioxidant properties, and Alzheimer's disease therapeutics. The manuscript underscores the critical importance of DSC in this field and the need for continued research to improve our understanding of these interactions, acting as a valuable resource for researchers.
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Affiliation(s)
- Pablo Zambrano
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.
| | - Marcela Manrique-Moreno
- Faculty of Natural of Exact Sciences, Chemistry Institute, University of Antioquia, A.A. 1226, Medellin, 050010, Antioquia, Colombia
| | - Karla Petit
- LabMAT, Department of Civil and Environmental Engineering, University of Bío-Bío, Concepción, Chile
| | - José R Colina
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Lientur 1457, Concepción 4080871, Chile
| | - Malgorzata Jemiola-Rzeminska
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Mario Suwalsky
- Facultad de Medicina, Universidad Católica de La Santísima Concepción, Concepción, Chile
| | - Kazimierz Strzalka
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
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Noro J, Vilaça-Faria H, Reis RL, Pirraco RP. Extracellular matrix-derived materials for tissue engineering and regenerative medicine: A journey from isolation to characterization and application. Bioact Mater 2024; 34:494-519. [PMID: 38298755 PMCID: PMC10827697 DOI: 10.1016/j.bioactmat.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/19/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024] Open
Abstract
Biomaterial choice is an essential step during the development tissue engineering and regenerative medicine (TERM) applications. The selected biomaterial must present properties allowing the physiological-like recapitulation of several processes that lead to the reestablishment of homeostatic tissue or organ function. Biomaterials derived from the extracellular matrix (ECM) present many such properties and their use in the field has been steadily increasing. Considering this growing importance, it becomes imperative to provide a comprehensive overview of ECM biomaterials, encompassing their sourcing, processing, and integration into TERM applications. This review compiles the main strategies used to isolate and process ECM-derived biomaterials as well as different techniques used for its characterization, namely biochemical and chemical, physical, morphological, and biological. Lastly, some of their applications in the TERM field are explored and discussed.
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Affiliation(s)
- Jennifer Noro
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Helena Vilaça-Faria
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui L. Reis
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rogério P. Pirraco
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
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Farzam F, Dabirmanesh B. Experimental techniques for detecting and evaluating the amyloid fibrils. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:183-227. [PMID: 38811081 DOI: 10.1016/bs.pmbts.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Amyloid fibrils are insoluble proteins with intricate β-sheet structures associated with various human diseases, including Parkinson's, Alzheimer's, and prion diseases. Proteins can form aggregates when their structure is misfolded, resulting in highly organized amyloid fibrils or amorphous aggregates. The formation of protein aggregates is a promising research field for mitigating diseases and the pharmaceutical and food industries. It is important to monitor and minimize the appearance of aggregates in these protein products. Several methods exist to assess protein aggregation, that includes from basic investigations to advanced biophysical techniques. Physicochemical parameters such as molecular weight, conformation, structure, and dimension are examined to study aggregation. There is an urgent need to develop methods for the detection of protein aggregation and amyloid fibril formation both in vitro and in vivo. This chapter focuses on a comprehensive discussion of the methods used to characterize and evaluate aggregates and amyloid fibrils.
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Affiliation(s)
- Farnoosh Farzam
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Barati A, Rezaei Somee L, Shahsavani MB, Ghasemi A, Hoshino M, Hong J, Saboury AA, Moosavi-Movahedi AA, Agnetti G, Yousefi R. Insights into the dual nature of αB-crystallin chaperone activity from the p.P39L mutant at the N-terminal region. Sci Rep 2024; 14:7353. [PMID: 38548822 PMCID: PMC10978848 DOI: 10.1038/s41598-024-57651-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 03/20/2024] [Indexed: 04/01/2024] Open
Abstract
The substitution of leucine to proline at position 39 (p.P39L) in human αB-crystallin (αB-Cry) has been associated with conflicting interpretations of pathogenicity in cataracts and cardiomyopathy. This study aimed to investigate the effects of the p.P39L mutation on the structural and functional features of human αB-Cry. The mutant protein was expressed in Escherichia coli (E. coli) and purified using anion exchange chromatography. We employed a wide range of spectroscopic analyses, gel electrophoresis, transmission electron microscopy (TEM), and atomic force microscopy (AFM) techniques to investigate the structure, function, stability, and fibrillation propensity of the mutant protein. The p.P39L mutation caused significant changes in the secondary, tertiary, and quaternary structures of human αB-Cry and increased the thermal stability of the protein. The mutant αB-Cry exhibited an increased chaperone activity and an altered oligomeric size distribution, along with an increased propensity to form amyloid aggregates. It is worth mentioning, increased chaperone activity has important positive and negative effects on damaged cells related to cataracts and cardiomyopathy, particularly by interfering in the process of apoptosis. Despite the apparent positive nature of the increased chaperone activity, it is also linked to adverse consequences. This study provides important insights into the effect of proline substitution by leucine at the N-terminal region on the dual nature of chaperone activity in human αB-Cry, which can act as a double-edged sword.
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Affiliation(s)
- Anis Barati
- Protein Chemistry Laboratory (PCL), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Leila Rezaei Somee
- Protein Chemistry Laboratory (PCL), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | | | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Masaru Hoshino
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Jun Hong
- School of Life Sciences, Henan University, Kaifeng, 475000, People's Republic of China
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | | | - Giulio Agnetti
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Reza Yousefi
- Protein Chemistry Laboratory (PCL), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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Dávalos AL, Rivera Echeverri JD, Favaro DC, Junio de Oliveira R, Penteado Battesini Carretero G, Lacerda C, Midea Cuccovia I, Cangussu Cardoso MV, Farah CS, Kopke Salinas R. Uncovering the Association Mechanism between Two Intrinsically Flexible Proteins. ACS Chem Biol 2024; 19:669-686. [PMID: 38486495 DOI: 10.1021/acschembio.3c00649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The understanding of protein-protein interaction mechanisms is key to the atomistic description of cell signaling pathways and for the development of new drugs. In this context, the mechanism of intrinsically disordered proteins folding upon binding has attracted attention. The VirB9 C-terminal domain (VirB9Ct) and the VirB7 N-terminal motif (VirB7Nt) associate with VirB10 to form the outer membrane core complex of the Type IV Secretion System injectisome. Despite forming a stable and rigid complex, VirB7Nt behaves as a random coil, while VirB9Ct is intrinsically dynamic in the free state. Here we combined NMR, stopped-flow fluorescence, and computer simulations using structure-based models to characterize the VirB9Ct-VirB7Nt coupled folding and binding mechanism. Qualitative data analysis suggested that VirB9Ct preferentially binds to VirB7Nt by way of a conformational selection mechanism at lower temperatures. However, at higher temperatures, energy barriers between different VirB9Ct conformations are more easily surpassed. Under these conditions the formation of non-native initial encounter complexes may provide alternative pathways toward the native complex conformation. These observations highlight the intimate relationship between folding and binding, calling attention to the fact that the two molecular partners must search for the most favored intramolecular and intermolecular interactions on a rugged and funnelled conformational energy landscape, along which multiple intermediates may lead to the final native state.
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Affiliation(s)
- Angy Liseth Dávalos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | | | - Denize C Favaro
- Department of Organic Chemistry, State University of Campinas, Campinas, 13083-862, Brazil
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York 10031, United States
| | - Ronaldo Junio de Oliveira
- Department of Physics, Institute of Exact, Natural and Educational Sciences, Federal University of Triângulo Mineiro, Uberaba, 38064-200, Brazil
| | | | - Caroline Lacerda
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Iolanda Midea Cuccovia
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | | | - Chuck S Farah
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Roberto Kopke Salinas
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
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11
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Eskew MW, Reardon P, Benight AS. DNA-based assay for calorimetric determination of protein concentrations in pure or mixed solutions. PLoS One 2024; 19:e0298969. [PMID: 38427623 PMCID: PMC10906865 DOI: 10.1371/journal.pone.0298969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024] Open
Abstract
It was recently reported that values of the transition heat capacities, as measured by differential scanning calorimetry, for two globular proteins and a short DNA hairpin in NaCl buffer are essentially equivalent, at equal concentrations (mg/mL). To validate the broad applicability of this phenomenon, additional evidence for this equivalence is presented that reveals it does not depend on DNA sequence, buffer salt, or transition temperature (Tm). Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm values. In all cases, evaluated protein concentrations determined from the DNA standard curves agreed with the UV-Vis concentration for monomeric proteins. For multimeric proteins evaluated concentrations were greater than determined by UV-Vis suggesting the calorimetric approach can also be an indicator of molecular stoichiometry.
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Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
| | - Patrick Reardon
- OSU NMR Facility, Oregon State University, Corvallis, Oregon, United States of America
| | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
- Department of Physics, Portland State University, Portland, Oregon, United States of America
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12
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Carvalho SF, Pereiro AB, Araújo JMM. Simultaneous Purification of Human Interferon Alpha-2b and Serum Albumin Using Bioprivileged Fluorinated Ionic Liquid-Based Aqueous Biphasic Systems. Int J Mol Sci 2024; 25:2751. [PMID: 38473998 DOI: 10.3390/ijms25052751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Interferon alpha-2b (IFN-α2b) is an essential cytokine widely used in the treatment of chronic hepatitis C and hairy cell leukemia, and serum albumin is the most abundant plasma protein with numerous physiological functions. Effective single-step aqueous biphasic system (ABS) extraction for the simultaneous purification of IFN-α2b and BSA (serum albumin protein) was developed in this work. Effects of the ionic liquid (IL)-based ABS functionalization, fluorinated ILs (FILs; [C2C1Im][C4F9SO3] and [N1112(OH)][C4F9SO3]) vs. mere fluoro-containing IL ([C4C1Im][CF3SO3]), in combination with sucrose or [N1112(OH)][H2PO4] (well-known globular protein stabilizers), or high-charge-density salt K3PO4 were investigated. The effects of phase pH, phase water content (%wt), phase composition (%wt), and phase volume ratio were investigated. The phase pH was found to have a significant effect on IFN-α2b and BSA partition. Experimental results show that simultaneous single-step purification was achieved with a high yield (extraction efficiency up to 100%) for both proteins and a purification factor of IFN-α2b high in the enriched IFN-α2b phase (up to 23.22) and low in the BSA-enriched phase (down to 0.00). SDS-PAGE analysis confirmed the purity of both recovered proteins. The stability and structure of IFN-α2b and BSA were preserved or even improved (FIL-rich phase) during the purification step, as evaluated by CD spectroscopy and DSC. Binding studies of IFN-α2b and BSA with the ABS phase-forming components were assessed by MST, showing the strong interaction between FILs aggregates and both proteins. In view of their biocompatibility, customizable properties, and selectivity, FIL-based ABSs are suggested as an improved purification step that could facilitate the development of biologics.
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Affiliation(s)
- Sara F Carvalho
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Ana B Pereiro
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - João M M Araújo
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
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13
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Ghade NS, Thappa DK, Lona J, Krishnan AR, Sonar SM. Comparative physicochemical and structural characterisation studies establish high biosimilarity between BGL-ASP and reference insulin aspart. Sci Rep 2024; 14:4224. [PMID: 38378730 PMCID: PMC10879530 DOI: 10.1038/s41598-024-54819-x] [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: 10/18/2023] [Accepted: 02/16/2024] [Indexed: 02/22/2024] Open
Abstract
Biosimilar insulin analogues are increasing market access for diabetic patients globally. Scientific establishment of biosimilarity is cornerstone of this key change in the medical landscape. BGL-ASP is a biosimilar insulin aspart developed by BioGenomics Limited, India. BioGenomics has considered a stepwise approach in generating the totality of evidence required to establish similarity with reference product. Insulin aspart is a recombinant rapid-acting human insulin analogue utilised in the treatment of type-1 and type-2 diabetes mellitus. The single amino acid substitution at position B28 where proline is replaced with aspartic acid results in a decreased propensity to form hexamers, thus increasing the absorption rate on subcutaneous administration compared to native insulin. In order to establish the safety and efficacy of BGL-ASP, the critical quality attributes (CQAs) of BGL-ASP are identified based on the impact created on biological activity, pharmacokinetic/pharmacodynamic (PK/PD), immunogenicity and safety. The CQAs of insulin aspart are related to product structure, purity and functionality and are characterised using a series of state-of-the-art orthogonal analytical tools. The primary protein sequence, the secondary, tertiary and quaternary structure are found to be highly similar for BGL-ASP and reference product. The product related impurities of insulin aspart and the assay content are determined using high performance liquid chromatography (HPLC) based analysis and is similar for BGL-ASP and reference insulin aspart sourced from United States of America (US), Europe Union (EU) and India. The safety, efficacy and immunogenicity of BGL-ASP is also found to be comparable with reference product and is confirmed through the clinical trials conducted as recommended by International Council for Harmonisation of Technical Requirements of Pharmaceuticals for Human Use (ICH) and European Medicines Agency (EMA) guidelines. The data encompassed in this study demonstrates that reference insulin aspart and BGL-ASP are highly similar in terms of structural, physicochemical, and biological properties, thus confirming its safety and efficacy for usage as potential alternative economical medicinal treatment for diabetes mellitus.
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Affiliation(s)
| | | | - Jeseena Lona
- BioGenomics Limited, Thane, Maharashtra, 400610, India
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14
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Ujfalusi-Pozsonyi K, Bódis E, Nyitrai M, Kengyel A, Telek E, Pécsi I, Fekete Z, Varnyuné Kis-Bicskei N, Mas C, Moussaoui D, Pernot P, Tully MD, Weik M, Schirò G, Kapetanaki SM, Lukács A. ATP-dependent conformational dynamics in a photoactivated adenylate cyclase revealed by fluorescence spectroscopy and small-angle X-ray scattering. Commun Biol 2024; 7:147. [PMID: 38307988 PMCID: PMC10837130 DOI: 10.1038/s42003-024-05842-1] [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: 06/17/2023] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Structural insights into the photoactivated adenylate cyclases can be used to develop new ways of controlling cellular cyclic adenosine monophosphate (cAMP) levels for optogenetic and other applications. In this work, we use an integrative approach that combines biophysical and structural biology methods to provide insight on the interaction of adenosine triphosphate (ATP) with the dark-adapted state of the photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata (OaPAC). A moderate affinity of the nucleotide for the enzyme was calculated and the thermodynamic parameters of the interaction have been obtained. Stopped-flow fluorescence spectroscopy and small-angle solution scattering have revealed significant conformational changes in the enzyme, presumably in the adenylate cyclase (AC) domain during the allosteric mechanism of ATP binding to OaPAC with small and large-scale movements observed to the best of our knowledge for the first time in the enzyme in solution upon ATP binding. These results are in line with previously reported drastic conformational changes taking place in several class III AC domains upon nucleotide binding.
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Affiliation(s)
- K Ujfalusi-Pozsonyi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - E Bódis
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - M Nyitrai
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - A Kengyel
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - E Telek
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - I Pécsi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Z Fekete
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | | | - C Mas
- Univ. Grenoble Alpes, CNRS, CEA, EMBL, ISBG, F-38000, Grenoble, France
| | - D Moussaoui
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - P Pernot
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - M D Tully
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - M Weik
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - G Schirò
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - S M Kapetanaki
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.
| | - A Lukács
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.
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15
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Sang Y, Huang X, Li H, Hong T, Zheng M, Li Z, Jiang Z, Ni H, Li Q, Zhu Y. Improving the thermostability of Pseudoalteromonas Porphyrae κ-carrageenase by rational design and MD simulation. AMB Express 2024; 14:8. [PMID: 38245573 PMCID: PMC10799840 DOI: 10.1186/s13568-024-01661-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/22/2024] Open
Abstract
The industrial applications of the κ-carrageenases have been restricted by their poor thermostability. In this study, based on the folding free energy change (ΔΔG) and the flexibility analysis using molecular dynamics (MD) simulation for the alkaline κ-carrageenase KCgCD from Pseudoalteromonas porphyrae (WT), the mutant S190R was identified with improved thermostability. After incubation at 50 °C for 30 min, the residual activity of S190R was 63.7%, 25.7% higher than that of WT. The Tm values determined by differential scanning calorimetry were 66.2 °C and 64.4 °C for S190R and WT, respectively. The optimal temperature of S190R was 10 °C higher than that of WT. The κ-carrageenan hydrolysates produced by S190R showed higher xanthine oxidase inhibitory activity compared with the untreated κ-carrageenan. MD simulation analysis of S190R showed that the residues (V186-M194 and P196-G197) in F5 and the key residue R150 in F3 displayed the decreased flexibility, and residues of T169-N173 near the catalytic center displayed the increased flexibility. These changed flexibilities might be the reasons for the improved thermostability of mutant S190R. This study provides a useful rational design strategy of combination of ΔΔG calculation and MD simulation to improve the κ-carrageenase's thermostability for its better industrial applications.
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Affiliation(s)
- Yuyan Sang
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
| | - Xiaoyi Huang
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
| | - Hebin Li
- Department of Pharmacy, Xiamen Medical College, 361008, Xiamen, China
| | - Tao Hong
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Mingjing Zheng
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Zhipeng Li
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Zedong Jiang
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Qingbiao Li
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Yanbing Zhu
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China.
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China.
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China.
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16
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Jain A, Kishore N. Glycation and drug binding by serum albumin. VITAMINS AND HORMONES 2024; 125:89-115. [PMID: 38997173 DOI: 10.1016/bs.vh.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Accumulation of glycation products in patients with hyperglycaemic conditions can lead to their reaction with the proteins in the human system such as serum albumin, haemoglobin, insulin, plasma lipoproteins, lens proteins and collagen among others which have important biological functions. Therefore, it is important to understand if glycation of these proteins affects their normal action not only qualitatively, but also importantly quantitatively. Glycation of human serum albumin can easily be carried out over period of weeks and its drug transportability may be examined, in addition to characterisation of the amadori products. A combination of ultrasensitive isothermal titration calorimetry, differential scanning calorimetry, spectroscopy and chromatography provides structure-property-energetics correlations which are important to obtain mechanistic aspects of drug recognition, conformation of the protein, and role of amadori products under conditions of glycation. The role of advance glycation end products is important in recognition of antidiabetic drugs. Further, the extent of glycation of the protein and its implication on drug transportability investigated by direct calorimetric methods enables unravelling mechanistic insights into role of functionality on drug molecules in the binding process, and hinderance in the recognition process, if any, as a result of glycation. It is possible that the drug binding ability of the protein under glycation conditions may not be adversely affected, or may even lead to strengthened ability. Rigorous studies on such systems with diverse functionality on the drug molecules is required which is essential in deriving guidelines for improvements in the existing drugs or in the synthesis of new molecular entities directed towards addressing diabetic conditions.
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Affiliation(s)
- Anu Jain
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India.
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17
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Malakoutikhah M, Mahran R, Gooran N, Masoumi A, Lundell K, Liljeblad A, Guiley K, Dai S, Zheng Q, Zhu L, Shokat KM, Kopra K, Härmä H. Nanomolar Protein Thermal Profiling with Modified Cyanine Dyes. Anal Chem 2023; 95:18344-18351. [PMID: 38060502 PMCID: PMC10733900 DOI: 10.1021/acs.analchem.3c02844] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023]
Abstract
Protein properties and interactions have been widely investigated by using external labels. However, the micromolar sensitivity of the current dyes limits their applicability due to the high material consumption and assay cost. In response to this challenge, we synthesized a series of cyanine5 (Cy5) dye-based quencher molecules to develop an external dye technique to probe proteins at the nanomolar protein level in a high-throughput one-step assay format. Several families of Cy5 dye-based quenchers with ring and/or side-chain modifications were designed and synthesized by introducing organic small molecules or peptides. Our results showed that steric hindrance and electrostatic interactions are more important than hydrophobicity in the interaction between the luminescent negatively charged europium-chelate-labeled peptide (Eu-probe) and the quencher molecules. The presence of substituents on the quencher indolenine rings reduces their quenching property, whereas the increased positive charge on the indolenine side chain improved the interaction between the quenchers and the luminescent compound. The designed quencher structures entirely altered the dynamics of the Eu-probe (protein-probe) for studying protein stability and interactions, as we were able to reduce the quencher concentration 100-fold. Moreover, the new quencher molecules allowed us to conduct the experiments using neutral buffer conditions, known as the peptide-probe assay. These improvements enabled us to apply the method in a one-step format for nanomolar protein-ligand interaction and protein profiling studies instead of the previously developed two-step protocol. These improvements provide a faster and simpler method with lower material consumption.
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Affiliation(s)
| | - Randa Mahran
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Negin Gooran
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Ahmadreza Masoumi
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Katri Lundell
- Laboratory
of Synthetic Drug Chemistry, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Arto Liljeblad
- Laboratory
of Synthetic Drug Chemistry, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Keelan Guiley
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
- Current
address: Rezo Therapeutics, Inc., San Francisco, California 94158, United States
| | - Shizhong Dai
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
- Current
address: Department of Genetics, Stanford
University, Stanford, California 94305, United States
| | - Qinheng Zheng
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Lawrence Zhu
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Kevan M. Shokat
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Kari Kopra
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Harri Härmä
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
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18
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Hada S, Burlakoti U, Kim KH, Han JS, Kim MJ, Kim NA, Jeong SH. A comprehensive evaluation of arginine and its derivatives as protein formulation stabilizers. Int J Pharm 2023; 647:123545. [PMID: 37871869 DOI: 10.1016/j.ijpharm.2023.123545] [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: 07/07/2023] [Revised: 10/14/2023] [Accepted: 10/21/2023] [Indexed: 10/25/2023]
Abstract
Arginine and its derivatives (such as arginine ethyl ester and acetyl arginine) have varying degrees of protein aggregation suppressor effect across different protein solutions. To understand this performance ambiguity, we evaluated the activity of arginine, acetyl arginine, and arginine ethyl ester for aggregation suppressor effect against human intravenous immunoglobulin G (IgG) solution at pH 4.8. Both arginine and its cationic derivative arginine ethyl ester in their hydrochloride salt forms significantly reduced the colloidal and conformational stability (reduced kd and Tm) of IgG. Consequently, the monomer content was decreased with an increase in subvisible particulates after agitation or thermal stress. Furthermore, compared to arginine, arginine ethyl ester with one more cationic charge and hydrochloride salt form readily precipitated IgG at temperatures higher than 25 °C. On the contrary, acetyl arginine, which mostly exists in a neutral state at pH 4.8, efficiently suppressed the formation of subvisible particles retaining a high amount of monomer owing to its higher colloidal and conformational stability. Concisely, the charged state of additives significantly impacts protein stability. This study demonstrated that contrary to popular belief, arginine and its derivatives may either enhance or suppress protein aggregation depending on their net charge and concentration.
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Affiliation(s)
- Shavron Hada
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Gyeonggi 10326, Republic of Korea.
| | - Urmila Burlakoti
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Gyeonggi 10326, Republic of Korea.
| | - Ki Hyun Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Gyeonggi 10326, Republic of Korea.
| | - Ji Soo Han
- Department of Pharmacy, College of Pharmacy, Mokpo National University, Muan 58554, Republic of Korea.
| | - Min Ji Kim
- Department of Pharmacy, College of Pharmacy, Mokpo National University, Muan 58554, Republic of Korea.
| | - Nam Ah Kim
- Department of Pharmacy, College of Pharmacy, Mokpo National University, Muan 58554, Republic of Korea; Department of Biomedicine, Health & Life Convergence Sciences, BK21 Four, Biomedical and Healthcare Research Institute, Mokpo National University, Muan 58554, Republic of Korea.
| | - Seong Hoon Jeong
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Gyeonggi 10326, Republic of Korea.
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19
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Lin Y, Moyle AB, Beaumont VA, Liu LL, Polleck S, Liu H, Shi H, Rouse JC, Kim HY, Zhang Y, Gross ML. Characterization of Higher Order Structural Changes of a Thermally Stressed Monoclonal Antibody via Mass Spectrometry Footprinting and Other Biophysical Approaches. Anal Chem 2023; 95:16840-16849. [PMID: 37933954 PMCID: PMC10909587 DOI: 10.1021/acs.analchem.3c02422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Characterizing changes in the higher order structure (HOS) of monoclonal antibodies upon stressed conditions is critical to gaining a better understanding of the product and process. One single biophysical approach may not be best suited to assess HOS comprehensively; thus, the synergy from multiple, complementary approaches improves characterization accuracy and resolution. In this study, we employed two mass spectrometry (MS )-based footprinting techniques, namely, fast photochemical oxidation of proteins (FPOP)-MS and hydrogen-deuterium exchange (HDX)-MS, supported by dynamic light scattering (DLS), differential scanning calorimetry (DSC), circular dichroism (CD), and nuclear magnetic resonance (NMR) to study changes to the HOS of a mAb upon thermal stress. The biophysical techniques report a nuanced characterization of the HOS in which CD detects no changes to the secondary or tertiary structure, yet DLS measurements show an increase in the hydrodynamic radius. DSC indicates that the stability decreases, and chemical or conformational changes accumulate with incubation time according to NMR. Furthermore, whereas HDX-MS does not indicate HOS changes, FPOP-MS footprinting reveals conformational changes at residue resolution for some amino acids. The local phenomena observed with FPOP-MS indicate that several residues show various patterns of degradation during thermal stress: no change, an increase in solvent exposure, and a biphasic response to solvent exposure. All evidences show that FPOP-MS efficiently resolves subtle structural changes and novel degradation pathways upon thermal stress treatment at residue-level resolution.
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Affiliation(s)
- Yanchun Lin
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
| | - Austin B Moyle
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
| | - Victor A Beaumont
- Pharmaceutical Sciences Small Molecules, Analytical Research and Development, Pfizer, Inc., Sandwich CT13 9FF, U.K
| | - Lucy L Liu
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Sharon Polleck
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Haijun Liu
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
| | - Heliang Shi
- Global Product Development, Rare Disease Statistics, Pfizer, Inc., New York, New York 10017, United States
| | - Jason C Rouse
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Hai-Young Kim
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Ying Zhang
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
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20
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D’Eusanio V, Morelli L, Marchetti A, Tassi L. Polyphenolic Compounds in Extracts from Roasted Grapevine Canes: An Investigation for a Circular Approach to Increase Sustainability in the Viticulture Sectors. Molecules 2023; 28:7676. [PMID: 38005398 PMCID: PMC10674344 DOI: 10.3390/molecules28227676] [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: 10/24/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023] Open
Abstract
In this study, we compared the polyphenolic composition of the roasted grapevine wood chips of four Vitis vinifera cultivars-namely, Sorbara, Grasparossa, Malbo Gentile, and Spergola. These waste byproducts have the potential as infusion chips for the aging of alcoholic beverages and vinegars, contributing to an enriched sensory profile. Roasting amplifies aromatic nuances and triggers the depletion of crucial bioactive compounds, including polyphenols. We investigated the extent of polyphenolic loss in the ethanolic extract of roasted grapevine chips to repurpose this waste byproduct and assess its potential. We assessed the levels of trans-resveratrol, trans-ε-viniferin, trans-piceatannol, and the main resveratrol trimer. Our findings indicated a significant decrease in polyphenol content as the roasting temperature increased, from 16.85-21.12 mg GAE/g for grapevine chips roasted at 120 °C to 3.10-7.77 mg GAE/g for those roasted at 240 °C. This study also highlights notable genotypic differences in polyphenolic content. Among the red grape cultivars analyzed, Sorbara exhibited the highest levels (7.77-21.12 mg/GAEg), whereas the white grape cultivar Spergola showed the lowest polyphenolic content (3.10-16.85 mg/GAEg). These findings not only contribute to the scientific understanding of polyphenol stability but also hold practical implications for the enhancement of aged beverages, as well as advancing sustainable practices in the viticulture industries.
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Affiliation(s)
- Veronica D’Eusanio
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (L.M.); (A.M.)
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Florence, Italy
| | - Lorenzo Morelli
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (L.M.); (A.M.)
| | - Andrea Marchetti
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (L.M.); (A.M.)
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Florence, Italy
- Interdepartmental Research Center BIOGEST-SITEIA, University of Modena and Reggio Emilia, 42121 Reggio Emilia, Italy
| | - Lorenzo Tassi
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy; (L.M.); (A.M.)
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Florence, Italy
- Interdepartmental Research Center BIOGEST-SITEIA, University of Modena and Reggio Emilia, 42121 Reggio Emilia, Italy
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21
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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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22
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Patel V, Aggarwal P, Sarvaiya J, Maity P, Ravichandiran V, Kaity S. Exploring novel and fast stability or sameness evaluation tool for different categories of injectable formulations. Eur J Pharm Sci 2023; 190:106551. [PMID: 37562551 DOI: 10.1016/j.ejps.2023.106551] [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: 12/05/2022] [Revised: 06/19/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023]
Abstract
The establishment of drug product stability and sameness is the heart of generic formulation development. For regulatory filing, various instrumental methods are used on a case basis to establish the generic and innovator product sameness in multiple aspects. Here in the present study, we explored the applicability of the Time-correlated single photon counting (TCS-PC) technique as a fast, reliable, and nondestructive method for establishing the sameness of three different categories of injectable formulations, namely, Amphotericin B liposome for injection, enoxaparin injection, and iron sucrose injection. All three category formulations were evaluated in their native and artificially induced post degradation state to identify the discrimination power of the used instrumental techniques. The degradation of materials were confirmed by high performance liquid chromatography (HPLC). Based on the product category, pre and post-degradation samples were evaluated by selective instrumental methods like differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR), fluorescence spectroscopy, particle size analysis by dynamic light scattering (DLS), small angle X-ray scattering (SAXS), Raman spectroscopy, inductively coupled plasma optical-emission spectrometry (ICP-OES) and circular dichroism study. All pre and post-degradation samples were further analyzed by TCS-PC. We observed that, TCS-PC can identify the differences between the initial and post degradation samples in very less time with promising discrimination power across the different injectable formulation types. Thus TCS-PC can be used as a fast and promising stability or sameness evaluation tool for different injectable drug products.
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Affiliation(s)
- Vaibhavi Patel
- School of Engineering and Technology, National Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Punita Aggarwal
- School of Engineering and Technology, National Forensic Sciences University, Gandhinagar, Gujarat, India; National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, West Bengal, India
| | - Jayrajsinh Sarvaiya
- Center of Excellence FTF, National Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Prasenjit Maity
- School of Engineering and Technology, National Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Velayutham Ravichandiran
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, West Bengal, India
| | - Santanu Kaity
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, West Bengal, India.
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23
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Lu D, Chen Y, Jiang M, Wang J, Li Y, Ma K, Sun W, Zheng X, Qi J, Jin W, Chen Y, Chai Y, Zhang CWH, Liang H, Tan S, Gao GF. KRAS G12V neoantigen specific T cell receptor for adoptive T cell therapy against tumors. Nat Commun 2023; 14:6389. [PMID: 37828002 PMCID: PMC10570350 DOI: 10.1038/s41467-023-42010-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
KRAS mutations are broadly recognized as promising targets for tumor therapy. T cell receptors (TCRs) can specifically recognize KRAS mutant neoantigens presented by human lymphocyte antigen (HLA) and mediate T cell responses to eliminate tumor cells. In the present study, we identify two TCRs specific for the 9-mer KRAS-G12V mutant neoantigen in the context of HLA-A*11:01. The TCR-T cells are constructed and display cytokine secretion and cytotoxicity upon co-culturing with varied tumor cells expressing the KRAS-G12V mutation. Moreover, 1-2C TCR-T cells show anti-tumor activity in preclinical models in female mice. The 9-mer KRAS-G12V mutant peptide exhibits a distinct conformation from the 9-mer wildtype peptide and its 10-mer counterparts. Specific recognition of the G12V mutant by TCR depends both on distinct conformation from wildtype peptide and on direct interaction with residues from TCRs. Our study reveals the mechanisms of presentation and TCR recognition of KRAS-G12V mutant peptide and describes TCRs with therapeutic potency for tumor immunotherapy.
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Affiliation(s)
- Dan Lu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Yuan Chen
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi, China
| | - Min Jiang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yiting Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Keke Ma
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Wenqiao Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xing Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenjing Jin
- YKimmu (Beijing) Biotechnology Co., Ltd, Beijing, China
| | - Yu Chen
- YKimmu (Beijing) Biotechnology Co., Ltd, Beijing, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | | | - Hao Liang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi, China
| | - Shuguang Tan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- Shenzhen Children's Hospital, Shenzhen, Guangdong, China.
- Beijing Life Science Academy, Beijing, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
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24
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Eskew MW, Reardon PW, Benight AS. Calorimetric analysis using DNA thermal stability to determine protein concentration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559360. [PMID: 37808849 PMCID: PMC10557601 DOI: 10.1101/2023.09.25.559360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
It was recently reported for two globular proteins and a short DNA hairpin in NaCl buffer that values of the transition heat capacities, Cp,DNA and Cp,PRO, for equal concentrations (mg/mL) of DNA and proteins, are essentially equivalent (differ by less than 1%). Additional evidence for this equivalence is presented that reveals this phenomenon does not depend on DNA sequence, buffer salt, or Tm. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm's. For the molecules, in NaCl and CsCl buffer the evaluated Cp,PRO and Cp,DNA were equivalent. Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. In all cases, evaluated protein concentrations determined from the DNA standard curve agreed with the UV-Vis concentration for monomeric proteins. For samples of multimeric proteins, streptavidin (tetramer), Herpes Simplex Virus glycoprotein D (trimer/dimer), and a 16 base pair DNA duplex (dimer), evaluated concentrations were greater than determined by UV-Vis by factors of 3.94, 2.65, and 2.15, respectively.
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Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
| | | | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
- Department of Physics, Portland State University, Portland, Oregon
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25
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Muller T, Bernier MÈ, Bazinet L. Optimization of Water Lentil (Duckweed) Leaf Protein Purification: Identification, Structure, and Foaming Properties. Foods 2023; 12:3424. [PMID: 37761132 PMCID: PMC10529404 DOI: 10.3390/foods12183424] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Water lentil, commonly known as duckweed, is an aquatic plant with great agronomic potential, as it can double its biomass in less than 24 h and contains up to 45% leaf proteins on a dry matter basis. However, extracting proteins from leaves is an arduous process due to the complexity of the matrix, which limits their uses in the food industry. In this study, water lentil protein extraction by solubilization was maximized using response surface methodology. By heating at 80 °C at pH 11 with a water lentil powder concentration of 2% or 4% for 2 h, up to 77.8% of total proteins were solubilized. Then, by precipitating the solubilized proteins at pH 4, a protein purity of 57.6% combined with a total protein yield of 60.0% was achieved. To the best of our knowledge, this is the highest leaf protein extraction yield reported in the literature with such protein purity. Proteomics analyses showed that the protein concentrate was composed of around 85.0% RubisCO, and protein structure analyses using ATR-FTIR and DSC were linked to a high protein solubility in water at pH 7. Moreover, a 1.5% protein solution of the protein concentrate at pH 7 showed excellent foaming properties compared to a 10.3% protein egg white solution. It had a superior foaming capacity (194% vs. 122%, respectively) for the same foaming stability after 60 min, which confirms water lentil proteins' potential for human nutrition and food formulation.
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Affiliation(s)
- Tristan Muller
- Institute of Nutrition and Functional Foods (INAF), Department of Food Sciences, Université Laval, Quebec, QC G1V 0A6, Canada; (T.M.); (M.-È.B.)
- Laboratoire de Transformation Alimentaire et Procédés Électro Membranaires (LTAPEM), Laboratory of Food Processing and Electro Membrane Processes, Université Laval, Quebec, QC G1V 0A6, Canada
| | - Marie-Ève Bernier
- Institute of Nutrition and Functional Foods (INAF), Department of Food Sciences, Université Laval, Quebec, QC G1V 0A6, Canada; (T.M.); (M.-È.B.)
- Laboratoire de Transformation Alimentaire et Procédés Électro Membranaires (LTAPEM), Laboratory of Food Processing and Electro Membrane Processes, Université Laval, Quebec, QC G1V 0A6, Canada
| | - Laurent Bazinet
- Institute of Nutrition and Functional Foods (INAF), Department of Food Sciences, Université Laval, Quebec, QC G1V 0A6, Canada; (T.M.); (M.-È.B.)
- Laboratoire de Transformation Alimentaire et Procédés Électro Membranaires (LTAPEM), Laboratory of Food Processing and Electro Membrane Processes, Université Laval, Quebec, QC G1V 0A6, Canada
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26
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Palma A, Rettenbacher LA, Moilanen A, Saaranen M, Pacheco-Martinez C, Gasser B, Ruddock L. Biochemical analysis of Komagataella phaffii oxidative folding proposes novel regulatory mechanisms of disulfide bond formation in yeast. Sci Rep 2023; 13:14298. [PMID: 37652992 PMCID: PMC10471769 DOI: 10.1038/s41598-023-41375-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023] Open
Abstract
Oxidative protein folding in the endoplasmic reticulum (ER) is driven mainly by protein disulfide isomerase PDI and oxidoreductin Ero1. Their activity is tightly regulated and interconnected with the unfolded protein response (UPR). The mechanisms of disulfide bond formation have mainly been studied in human or in the yeast Saccharomyces cerevisiae. Here we analyze the kinetics of disulfide bond formation in the non-conventional yeast Komagataella phaffii, a common host for the production of recombinant secretory proteins. Surprisingly, we found significant differences with both the human and S. cerevisiae systems. Specifically, we report an inactive disulfide linked complex formed by K. phaffii Ero1 and Pdi1, similarly to the human orthologs, but not described in yeast before. Furthermore, we show how the interaction between K. phaffii Pdi1 and Ero1 is unaffected by the introduction of unfolded substrate into the system. This is drastically opposed to the previously observed behavior of the human pathway, suggesting a different regulation of the UPR and/or possibly different interaction mechanics between K. phaffii Pdi1 and Ero1.
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Affiliation(s)
- Arianna Palma
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Lukas A Rettenbacher
- School of Biosciences, University of Kent, Canterbury, UK
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Antti Moilanen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Mirva Saaranen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Brigitte Gasser
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.
- Austrian Centre of Industrial Biotechnology, Vienna, Austria.
| | - Lloyd Ruddock
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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27
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Chou Y, Hsieh C, Chen Y, Wang T, Wu W, Hwang C. Characterization of the pH-dependent protein stability of 3α-hydroxysteroid dehydrogenase/carbonyl reductase by differential scanning fluorimetry. Protein Sci 2023; 32:e4710. [PMID: 37354013 PMCID: PMC10357940 DOI: 10.1002/pro.4710] [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: 05/03/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023]
Abstract
The characterization of protein stability is essential for understanding the functions of proteins. Hydroxysteroid dehydrogenase is involved in the biosynthesis of steroid hormones and the detoxification of xenobiotic carbonyl compounds. However, the stability of hydroxysteroid dehydrogenases has not yet been characterized in detail. Here, we determined the changes in Gibbs free energy, enthalpy, entropy, and heat capacity of unfolding for 3α-hydroxysteroid dehydrogenase/carbonyl reductase (3α-HSD/CR) by varying the pH and urea concentration through differential scanning fluorimetry and presented pH-dependent protein stability as a function of temperature. 3α-HSD/CR shows the maximum stability of 30.79 kJ mol-1 at 26.4°C, pH 7.6 and decreases to 7.74 kJ mol-1 at 25.7°C, pH 4.5. The change of heat capacity of 30.25 ± 1.38 kJ mol-1 K-1 is obtained from the enthalpy of denaturation as a function of melting temperature at varied pH. Two proton uptakes are linked to protein unfolding from residues with differential pKa of 4.0 and 6.5 in the native and denatured states, respectively. The large positive heat capacity change indicated that hydrophobic interactions played an important role in the folding of 3α-HSD/CR. These studies reveal the mechanism of protein unfolding in HSD and provide a convenient method to extract thermodynamic parameters for characterizing protein stability using differential scanning fluorimetry.
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Affiliation(s)
- Yun‐Hao Chou
- Graduate Institute of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan
| | - Chia‐Lin Hsieh
- Graduate Institute of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan
| | - Yan‐Liang Chen
- Graduate Institute of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan
| | - Tzu‐Pin Wang
- Department of Medicinal and Applied ChemistryKaohsiung Medical UniversityKaohsiungTaiwan
| | - Wen‐Jeng Wu
- Department of Urology, Chung‐Ho Memorial HospitalKaohsiung Medical UniversityKaohsiungTaiwan
| | - Chi‐Ching Hwang
- Graduate Institute of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan
- Department of Biochemistry, Faculty of Medicine, College of MedicineKaohsiung Medical UniversityKaohsiungTaiwan
- Department of Medical ResearchKaohsiung Medical University HospitalKaohsiungTaiwan
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28
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Garcia-Villen F, Gallego I, Sainz-Ramos M, Ordoyo-Pascual J, Ruiz-Alonso S, Saenz-del-Burgo L, O’Mahony C, Pedraz JL. Stability of Monoclonal Antibodies as Solid Formulation for Auto-Injectors: A Pilot Study. Pharmaceutics 2023; 15:2049. [PMID: 37631263 PMCID: PMC10459033 DOI: 10.3390/pharmaceutics15082049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Drug adherence is a significant medical issue, often responsible for sub-optimal outcomes during the treatment of chronic diseases such as rheumatoid or psoriatic arthritis. Monoclonal antibodies (which are exclusively given parenterally) have been proven to be an effective treatment in these cases. The use of auto-injectors is an effective strategy to improve drug adherence in parenteral treatments since these pen-like devices offer less discomfort and increased user-friendliness over conventional syringe-based delivery. This study aims to investigate the feasibility of including a monoclonal antibody as a solid formulation inside an auto-injector pen. Specifically, the objective was to evaluate the drug stability after a concentration (to reduce the amount of solvent and space needed) and freeze-drying procedure. A preliminary screening of excipients to improve stability was also performed. The nano-DSC results showed that mannitol improved the stability of the concentrated, freeze-dried antibody in comparison to its counterpart without it. However, a small instability of the CH2 domain was still found for mannitol samples, which will warrant further investigation. The present results serve as a stepping stone towards advancing future drug delivery systems that will ultimately improve the patient experience and associated drug adherence.
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Affiliation(s)
- Fatima Garcia-Villen
- NanoBioCel Group, Laboratory of Pharmaceutics, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain (L.S.-d.-B.)
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Institute of Health Carlos III, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Resarch Group, 01009 Vitoria-Gasteiz, Spain
| | - Idoia Gallego
- NanoBioCel Group, Laboratory of Pharmaceutics, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain (L.S.-d.-B.)
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Institute of Health Carlos III, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Resarch Group, 01009 Vitoria-Gasteiz, Spain
| | - Myriam Sainz-Ramos
- NanoBioCel Group, Laboratory of Pharmaceutics, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain (L.S.-d.-B.)
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Institute of Health Carlos III, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Resarch Group, 01009 Vitoria-Gasteiz, Spain
| | - Jorge Ordoyo-Pascual
- NanoBioCel Group, Laboratory of Pharmaceutics, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain (L.S.-d.-B.)
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Institute of Health Carlos III, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Resarch Group, 01009 Vitoria-Gasteiz, Spain
| | - Sandra Ruiz-Alonso
- NanoBioCel Group, Laboratory of Pharmaceutics, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain (L.S.-d.-B.)
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Institute of Health Carlos III, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Resarch Group, 01009 Vitoria-Gasteiz, Spain
| | - Laura Saenz-del-Burgo
- NanoBioCel Group, Laboratory of Pharmaceutics, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain (L.S.-d.-B.)
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Institute of Health Carlos III, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Resarch Group, 01009 Vitoria-Gasteiz, Spain
| | - Conor O’Mahony
- Tyndall National Institute, University College Cork, T12 R5CP Cork, Ireland;
| | - Jose Luis Pedraz
- NanoBioCel Group, Laboratory of Pharmaceutics, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain (L.S.-d.-B.)
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Institute of Health Carlos III, 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Resarch Group, 01009 Vitoria-Gasteiz, Spain
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29
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Wijker S, Palmans ARA. Protein-Inspired Control over Synthetic Polymer Folding for Structured Functional Nanoparticles in Water. Chempluschem 2023; 88:e202300260. [PMID: 37417828 DOI: 10.1002/cplu.202300260] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
The folding of proteins into functional nanoparticles with defined 3D structures has inspired chemists to create simple synthetic systems mimicking protein properties. The folding of polymers into nanoparticles in water proceeds via different strategies, resulting in the global compaction of the polymer chain. Herein, we review the different methods available to control the conformation of synthetic polymers and collapse/fold them into structured, functional nanoparticles, such as hydrophobic collapse, supramolecular self-assembly, and covalent cross-linking. A comparison is made between the design principles of protein folding to synthetic polymer folding and the formation of structured nanocompartments in water, highlighting similarities and differences in design and function. We also focus on the importance of structure for functional stability and diverse applications in complex media and cellular environments.
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Affiliation(s)
- Stefan Wijker
- Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Anja R A Palmans
- Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
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30
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Wales DJ. Energy Landscapes and Heat Capacity Signatures for Monomers and Dimers of Amyloid-Forming Hexapeptides. Int J Mol Sci 2023; 24:10613. [PMID: 37445791 DOI: 10.3390/ijms241310613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Amyloid formation is a hallmark of various neurodegenerative disorders. In this contribution, energy landscapes are explored for various hexapeptides that are known to form amyloids. Heat capacity (CV) analysis at low temperature for these hexapeptides reveals that the low energy structures contributing to the first heat capacity feature above a threshold temperature exhibit a variety of backbone conformations for amyloid-forming monomers. The corresponding control sequences do not exhibit such structural polymorphism, as diagnosed via end-to-end distance and a dihedral angle defined for the monomer. A similar heat capacity analysis for dimer conformations obtained using basin-hopping global optimisation shows clear features in end-to-end distance versus dihedral correlation plots, where amyloid-forming sequences exhibit a preference for larger end-to-end distances and larger positive dihedrals. These results hold true for sequences taken from tau, amylin, insulin A chain, a de novo designed peptide, and various control sequences. While there is a little overall correlation between the aggregation propensity and the temperature at which the low-temperature CV feature occurs, further analysis suggests that the amyloid-forming sequences exhibit the key CV feature at a lower temperature compared to control sequences derived from the same protein.
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Affiliation(s)
- David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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31
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Puri S, Liu CY, Hu IC, Lai CH, Hsu STD, Lyu PC. Elucidation of the folding pathway of a circular permutant of topologically knotted YbeA by tryptophan substitutions. Biochem Biophys Res Commun 2023; 672:81-88. [PMID: 37343318 DOI: 10.1016/j.bbrc.2023.06.021] [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: 05/29/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
CP74 is an engineered circular permutant of a deep trefoil knotted SpoU-TrmD (SPOUT) RNA methyl transferase protein YbeA from E. coli. We have previously established that the circular permutation unties the knotted topology of YbeA and CP74 forms a domain-swapped dimer with a large dimeric interface of ca. 4600 Å2. To understand the impact of domain-swapping and the newly formed hinge region joining the two folded domains on the folding and stability of CP74, the five equally spaced tryptophan residues were individually substituted into phenylalanine to monitor their conformational and stability changes by a battery of biophysical tools. Far-UV circular dichroism, intrinsic fluorescence, and small-angle X-ray scattering dictated minimal global conformational perturbations to the native structures in the tryptophan variants. The structures of the tryptophan variants also showed the conservation of the domain-swapped ternary structure with the exception that the W72F exhibited significant asymmetry in the α-helix 5. Comparative global thermal and chemical stability analyses indicated the pivotal role of W100 in the folding of CP74 followed by W19 and W72. Solution-state NMR spectroscopy and hydrogen-deuterium exchange mass spectrometry further revealed the accumulation of a native-like intermediate state in which the hinge region made important contributions to maintain the domain-swapped ternary structure of CP74.
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Affiliation(s)
- Sarita Puri
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Yu Liu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - I-Chen Hu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashihiroshima, 739-8527, Japan.
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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Arauzo-Aguilera K, Buscajoni L, Koch K, Thompson G, Robinson C, Berkemeyer M. Yields and product comparison between Escherichia coli BL21 and W3110 in industrially relevant conditions: anti-c-Met scFv as a case study. Microb Cell Fact 2023; 22:104. [PMID: 37208750 PMCID: PMC10197847 DOI: 10.1186/s12934-023-02111-4] [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: 01/17/2023] [Accepted: 05/01/2023] [Indexed: 05/21/2023] Open
Abstract
INTRODUCTION In the biopharmaceutical industry, Escherichia coli is one of the preferred expression hosts for large-scale production of therapeutic proteins. Although increasing the product yield is important, product quality is a major factor in this industry because greatest productivity does not always correspond with the highest quality of the produced protein. While some post-translational modifications, such as disulphide bonds, are required to achieve the biologically active conformation, others may have a negative impact on the product's activity, effectiveness, and/or safety. Therefore, they are classified as product associated impurities, and they represent a crucial quality parameter for regulatory authorities. RESULTS In this study, fermentation conditions of two widely employed industrial E. coli strains, BL21 and W3110 are compared for recombinant protein production of a single-chain variable fragment (scFv) in an industrial setting. We found that the BL21 strain produces more soluble scFv than the W3110 strain, even though W3110 produces more recombinant protein in total. A quality assessment on the scFv recovered from the supernatant was then performed. Unexpectedly, even when our scFv is correctly disulphide bonded and cleaved from its signal peptide in both strains, the protein shows charge heterogeneity with up to seven distinguishable variants on cation exchange chromatography. Biophysical characterization confirmed the presence of altered conformations of the two main charged variants. CONCLUSIONS The findings indicated that BL21 is more productive for this specific scFv than W3110. When assessing product quality, a distinctive profile of the protein was found which was independent of the E. coli strain. This suggests that alterations are present in the recovered product although the exact nature of them could not be determined. This similarity between the two strains' generated products also serves as a sign of their interchangeability. This study encourages the development of innovative, fast, and inexpensive techniques for the detection of heterogeneity while also provoking a debate about whether intact mass spectrometry-based analysis of the protein of interest is sufficient to detect heterogeneity in a product.
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Affiliation(s)
| | - Luisa Buscajoni
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Karin Koch
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Gary Thompson
- Wellcome Trust Biological NMR Facility, School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Colin Robinson
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Matthias Berkemeyer
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
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Hu Z, Wang Y, Ma Z, Cheng T, Guo Z, Zhou L, Wang Z. Impacts of Industrial Modification on the Structure and Gel Features of Soy Protein Isolate and its Composite Gel with Myofibrillar Protein. Foods 2023; 12:foods12101982. [PMID: 37238801 DOI: 10.3390/foods12101982] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Native soy protein isolate (N-SPI) has a low denaturation point and low solubility, limiting its industrial application. The influence of different industrial modification methods (heat (H), alkaline (A), glycosylation (G), and oxidation (O)) on the structure of SPI, the properties of the gel, and the gel properties of soy protein isolate (SPI) in myofibril protein (MP) was evaluated. The study found that four industrial modifications did not influence the subunit composition of SPI. However, the four industrial modifications altered SPI's secondary structure and disulfide bond conformation content. A-SPI exhibits the highest surface hydrophobicity and I850/830 ratio but the lowest thermal stability. G-SPI exhibits the highest disulfide bond content and the best gel properties. Compared with MP gel, the addition of H-SPI, A-SPI, G-SPI, and O-SPI components significantly improved the properties of the gel. Additionally, MP-ASPI gel exhibits the best properties and microstructure. Overall, the four industrial modification effects may impact SPI's structure and gel properties in different ways. A-SPI could be a potential functionality-enhanced soy protein ingredient in comminuted meat products. The present study results will provide a theoretical basis for the industrialized production of SPI.
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Affiliation(s)
- Zhaodong Hu
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
- College of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Yichang Wang
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Zihan Ma
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Tianfu Cheng
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Zengwang Guo
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Linyi Zhou
- College of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Zhongjiang Wang
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
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D'Eusanio V, Genua F, Marchetti A, Morelli L, Tassi L. Characterization of Some Stilbenoids Extracted from Two Cultivars of Lambrusco- Vitis vinifera Species: An Opportunity to Valorize Pruning Canes for a More Sustainable Viticulture. Molecules 2023; 28:molecules28104074. [PMID: 37241814 DOI: 10.3390/molecules28104074] [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: 04/19/2023] [Revised: 05/04/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Pruning canes from grape vines are valuable byproducts that contain resveratrol and other health-boosting stilbenoids. This study aimed to assess the effect of roasting temperature on the stilbenoid content of vine canes by comparing two Vitis vinifera cultivars, Lambrusco Ancellotta and Salamino. Samples were collected during different phases of the vine plant cycle. One set was collected in September after the grape harvest and was air-dried and analyzed. A second set was obtained during vine pruning in February and evaluated immediately after collection. The main stilbenoid identified in each sample was resveratrol (~100-2500 mg/kg), with significant levels of viniferin (~100-600 mg/kg) and piceatannol (~0-400 mg/kg). Their contents decreased with increasing roasting temperature and residence time on the plant. This study provides valuable insights into the use of vine canes in a novel and efficient manner, which could potentially benefit different industries. One potential use involves the roasted cane chips to accelerate the aging of vinegars and alcoholic beverages. This method is more efficient and cost-effective than traditional aging, which is slow and unfavorable from an industrial perspective. Furthermore, incorporating vine canes into maturation processes reduces viticulture waste and enhances the final products with health-promoting molecules, such as resveratrol.
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Affiliation(s)
- Veronica D'Eusanio
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Florence, Italy
| | - Francesco Genua
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Andrea Marchetti
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Florence, Italy
- Interdepartmental Research Center BIOGEST-SITEIA, University of Modena and Reggio Emilia, 42121 Reggio Emilia, Italy
| | - Lorenzo Morelli
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Lorenzo Tassi
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Florence, Italy
- Interdepartmental Research Center BIOGEST-SITEIA, University of Modena and Reggio Emilia, 42121 Reggio Emilia, Italy
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35
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Swamy MJ, Mondal S. Subunit association, and thermal and chemical unfolding of Cucurbitaceae phloem exudate lectins. A review. Int J Biol Macromol 2023; 233:123434. [PMID: 36709810 DOI: 10.1016/j.ijbiomac.2023.123434] [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: 10/31/2022] [Revised: 01/13/2023] [Accepted: 01/22/2023] [Indexed: 01/27/2023]
Abstract
Detailed characterization of protein (un)folding intermediates is crucial for understanding the (un)folding pathway, aggregation, stability and their functional properties. In recent years, stress-inducible lectins are being investigated with much interest. In plants phloem proteins PP1 and PP2 are major components of the phloem fluid. While PP1 is a structural protein, PP2 exhibits lectin activity, and was proposed to play key roles in wound sealing, anti-pathogenic activity, and transportation of various molecules including RNA within the plant. Cucurbitaceae fruits contain high concentrations of PP2 lectins, which recognize chitooligosaccharides with high specificity. Although the presence of PP2 lectins in the phloem exudate of Cucurbitaceae species was documented over 40 years ago, so far only a few proteins from this family have been purified and characterized in detail. This review summarizes the results of biophysical studies aimed at investigating the oligomeric status of these lectins, their thermal stability, structural perturbations caused by changes in pH and addition of chaotropic agents and characterization of intermediates observed in the unfolding process. The implications of these results in the functional roles played by PP2 type lectins in their native environment are discussed. Finally, perspectives for future biophysical research on these proteins are given.
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Affiliation(s)
- Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India.
| | - Saradamoni Mondal
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
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36
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Tomimoto Y, Yamazaki R, Shirai H. Increasing the melting temperature of VHH with the in silico free energy score. Sci Rep 2023; 13:4922. [PMID: 36966210 PMCID: PMC10039853 DOI: 10.1038/s41598-023-32022-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/21/2023] [Indexed: 03/27/2023] Open
Abstract
VHH, the antigen-binding fragment of a heavy chain-only antibody, is a useful component of antibody-based therapeutics. Thermal stability, represented by the melting temperature (Tm), is one of the key factors affecting the developability of antibody-based therapeutics. In this study, we examined whether the in silico free energy score dStability can be used to design mutants with improved Tm compared to the anti-lysozyme VHH, D3-L11. After verifying that exhaustive mutagenesis was inefficient for improving Tm, we performed a two-round rational approach that combined dStability calculations with a small number of experiments. This method improved the Tm by more than 5 °C in several single mutants including A79I. It reduced the affinity for the antigen by less than 1.6-fold. We speculate that stabilization of A79I required exquisite compatibility among neighboring residues to fill in the internal cavity in the protein. Given that we identified only one mutation that could simultaneously improve Tm and almost maintain affinity, we concluded that achieving both is extremely difficult, even with single mutations that are not located in the paratope. Therefore, we recommend using a variety of approaches when trying to achieve such a feat. Our method will be a useful complementary approach to other existing methods.
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Affiliation(s)
- Yusuke Tomimoto
- Applied Research and Operations, Astellas Pharma Inc., Tsukuba city, Ibaraki, 305-8585, Japan
| | - Rika Yamazaki
- Applied Research and Operations, Astellas Pharma Inc., Tsukuba city, Ibaraki, 305-8585, Japan
| | - Hiroki Shirai
- Applied Research and Operations, Astellas Pharma Inc., Tsukuba city, Ibaraki, 305-8585, Japan.
- Riken Center for Computational Science, Nihonbashi 1-Chome Mitsui Building, 15th floor, 1-4-1 Nihonbashi, Tsukuba, 103-0027, Japan.
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37
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Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
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Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
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38
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Västberg A, Bolinsson H, Leeman M, Nilsson L, Nylander T, Sejwal K, Sintorn IM, Lidayova K, Sjögren H, Wahlgren M, Elofsson U. Investigating Thermally Induced Aggregation of Somatropin- New Insights Using Orthogonal Techniques. Int J Pharm 2023; 637:122829. [PMID: 36948472 DOI: 10.1016/j.ijpharm.2023.122829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/24/2023]
Abstract
Three orthogonal techniques were used to provide new insights into thermally induced aggregation of the therapeutic protein Somatropin at pH 5.8 and 7.0. The techniques were Dynamic Light Scattering (DLS), Asymmetric Flow-Field Flow-Fractionation (AF4), and the TEM-based analysis system MiniTEM™. In addition, Differential Scanning Calorimetry (DSC) was used to study the thermal unfolding and stability. DSC and DLS were used to explain the initial aggregation process and aggregation rate at the two pH values. The results suggest that electrostatic stabilization seems to be the main reason for the faster initial aggregation at pH 5.8, i.e., closer to the isoelectric point of Somatropin. AF4 and MiniTEM were used to investigate the aggregation pathway further. Combining the results allowed us to demonstrate Somatropin's thermal aggregation pathway at pH 7.0. The growth of the aggregates appears to follow two steps. Smaller elongated aggregates are formed in the first step, possibly initiated by partly unfolded species. In the second step, occurring during longer heating, the smaller aggregates assemble into larger aggregates with more complex structures.
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Affiliation(s)
- Amanda Västberg
- Research Institutes of Sweden, Drottning Kristinas väg 61B, 11428 Stockholm, Sweden; Department of Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Hans Bolinsson
- Department of Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | | | - Lars Nilsson
- Department of Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Tommy Nylander
- Physical Chemistry, Department of Chemistry, Lund University, Lund, Sweden
| | | | | | | | | | - Marie Wahlgren
- Department of Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Ulla Elofsson
- Research Institutes of Sweden, Drottning Kristinas väg 61B, 11428 Stockholm, Sweden
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39
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Lin HJL, Parkinson DH, Holman JC, Thompson WC, Anderson CNK, Hadfield M, Ames S, Zuniga Pina NR, Bowden JN, Quinn C, Hansen LD, Price JC. Modification of the structural stability of human serum albumin in rheumatoid arthritis. PLoS One 2023; 18:e0271008. [PMID: 36930604 PMCID: PMC10022781 DOI: 10.1371/journal.pone.0271008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/29/2022] [Indexed: 03/18/2023] Open
Abstract
Differential scanning calorimetry (DSC) can indicate changes in structure and/or concentration of the most abundant proteins in a biological sample via heat denaturation curves (HDCs). In blood serum for example, HDC changes result from either concentration changes or altered thermal stabilities for 7-10 proteins and has previously been shown capable of differentiating between sick and healthy human subjects. Here, we compare HDCs and proteomic profiles of 50 patients experiencing joint-inflammatory symptoms, 27 of which were clinically diagnosed with rheumatoid arthritis (RA). The HDC of all 50 subjects appeared significantly different from expected healthy curves, but comparison of additional differences between the RA and the non-RA subjects allowed more specific understanding of RA samples. We used mass spectrometry (MS) to investigate the reasons behind the additional HDC changes observed in RA patients. The HDC differences do not appear to be directly related to differences in the concentrations of abundant serum proteins. Rather, the differences can be attributed to modified thermal stability of some fraction of the human serum albumin (HSA) proteins in the sample. By quantifying differences in the frequency of artificially induced post translational modifications (PTMs), we found that HSA in RA subjects had a much lower surface accessibility, indicating potential ligand or protein binding partners in certain regions that could explain the shift in HSA melting temperature in the RA HDCs. Several low abundance proteins were found to have significant changes in concentration in RA subjects and could be involved in or related to binding of HSA. Certain amino acid sites clusters were found to be less accessible in RA subjects, suggesting changes in HSA structure that may be related to changes in protein-protein interactions. These results all support a change in behavior of HSA which may give insight into mechanisms of RA pathology.
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Affiliation(s)
- Hsien-Jung L. Lin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - David H. Parkinson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - J. Connor Holman
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - W. Chad Thompson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Christian N. K. Anderson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Marcus Hadfield
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Stephen Ames
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Nathan R. Zuniga Pina
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Jared N. Bowden
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Colette Quinn
- Applications Lab, TA Instruments, Lindon, Utah, United States of America
| | - Lee D. Hansen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - John C. Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
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40
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Digby ZA, Chen Y, Akkaoui K, Schlenoff JB. Bulk Biopolyelectrolyte Complexes from Homopolypeptides: Solid "Salt Bridges". Biomacromolecules 2023; 24:1453-1462. [PMID: 36753621 DOI: 10.1021/acs.biomac.2c01456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Salt bridges, pairings between oppositely charged amino acids, are dispersed throughout proteins to assist folding and interactions. Biopolyelectrolyte complexes (BioPECs) were made between the homopolypeptides poly-l-arginine (PLR) and poly-l-lysine (PLK) with sodium triphosphate (STPP), as well as from polypeptide-only combinations. Viscoelastic measurements on these high salt bridge density materials showed many were solid, even glassy, in nature. Although the polypeptide-phosphate complexes had similar moduli at room temperature, the PLR-STPP complex displayed an unusual melting event above 70 °C not seen in PLK-STPP. This event was supported with differential scanning calorimetry. Infrared spectroscopy showed the PLK-STPP system contained β-sheets, while PLR-STPP did not. Stoichiometric, macroscopic BioPECs of PLR and PLK with poly-l-aspartic acid (PLD) and poly-l-glutamic acid (PLE) were made. PLR-PLD was found to undergo a melting event similar to that in PLR-STPP. ATR-FTIR studies showed that BioPECs made with PLD do not contain β-sheets, while those composed of PLE do. This work illustrates an expanded palette of unique properties from these biomaterials, such as strong viscoelastic differences between PECs containing PLE and PLD, even though they differ by only one carbon on the side chain.
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Affiliation(s)
- Zachary A Digby
- Department of Chemistry and Biochemistry The Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Yuhui Chen
- Department of Chemistry and Biochemistry The Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Khalil Akkaoui
- Department of Chemistry and Biochemistry The Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Joseph B Schlenoff
- Department of Chemistry and Biochemistry The Florida State University, Tallahassee, Florida 32306-4390, United States
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41
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Goulding DA, Bovetto L, O'Regan J, O'Brien NM, O'Mahony JA. Heteroprotein complex coacervation of lactoferrin and osteopontin: Phase behaviour and thermodynamics of formation. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2022.108216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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42
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Rottenaicher GJ, Absmeier RM, Meier L, Zacharias M, Buchner J. A constant domain mutation in a patient-derived antibody light chain reveals principles of AL amyloidosis. Commun Biol 2023; 6:209. [PMID: 36823438 PMCID: PMC9950467 DOI: 10.1038/s42003-023-04574-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Light chain (AL) amyloidosis is a debilitating disease in which mutant antibody light chains (LC), secreted by aberrant plasma cell clones, misfold and form insoluble fibrils, which can be deposited in various organs. In the majority of cases, the fibrillar deposits consist of LC variable domains (VL) containing destabilizing mutations compared to their germline counterparts. This is also true for the patient LC FOR005. However, this pathogenic LC sequence contains an additional mutation in the constant domain (CL). The mechanistic impact of CL mutations is not yet understood in the context of AL amyloidosis. Our analysis reveals that the FOR005 CL mutation influences the amyloid pathway in specific ways: (1) folding and stability of the patient CL domain are strongly impaired; (2) the mutation disrupts the LC dimer interface and weakens dimerization; (3) the CL mutation promotes proteolytic cleavage of the LC monomers resulting in an isolated, amyloidogenic VL domain while dimeric LCs are not cleaved. The enhanced proteolysis rates and the inability of full-length LCs to form amyloid fibrils even in the presence of a destabilized CL domain support a model for AL amyloidosis in which the CL domain plays a protective role and in which proteolytic cleavage precedes amyloid formation.
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Affiliation(s)
- Georg J Rottenaicher
- Center for Functional Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
- Department of Biosciences, TUM School of Natural Sciences, Technical University Munich, Boltzmannstr. 10, 85748, Garching, Germany
| | - Ramona M Absmeier
- Center for Functional Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
- Department of Biosciences, TUM School of Natural Sciences, Technical University Munich, Boltzmannstr. 10, 85748, Garching, Germany
| | - Laura Meier
- Center for Functional Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
- Department of Biosciences, TUM School of Natural Sciences, Technical University Munich, Boltzmannstr. 10, 85748, Garching, Germany
| | - Martin Zacharias
- Center for Functional Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
- Department of Biosciences, TUM School of Natural Sciences, Technical University Munich, Boltzmannstr. 10, 85748, Garching, Germany
| | - Johannes Buchner
- Center for Functional Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany.
- Department of Biosciences, TUM School of Natural Sciences, Technical University Munich, Boltzmannstr. 10, 85748, Garching, Germany.
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43
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Rivera M, Mjaavatten A, Smith SB, Baez M, Wilson CAM. Temperature dependent mechanical unfolding and refolding of a protein studied by thermo-regulated optical tweezers. Biophys J 2023; 122:513-521. [PMID: 36587240 PMCID: PMC9941719 DOI: 10.1016/j.bpj.2022.12.034] [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: 02/07/2022] [Revised: 06/15/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
Temperature is a useful system variable to gather kinetic and thermodynamic information from proteins. Usually, free energy and the associated entropic and enthalpic contributions are obtained by quantifying the conformational equilibrium based on melting experiments performed in bulk conditions. Such experiments are suitable only for those small single-domain proteins whose side reactions of irreversible aggregation are unlikely to occur. Here, we avoid aggregation by pulling single-protein molecules in a thermo-regulated optical tweezers. Thus, we are able to explore the temperature dependence of the thermodynamic and kinetic parameters of MJ0366 from Methanocaldococcus jannaschii at the single-molecule level. By performing force-ramp experiments between 2°C and 40°C, we found that MJ0366 has a nonlinear dependence of free energy with temperature and a specific heat change of 2.3 ± 1.2 kcal/mol∗K. These thermodynamic parameters are compatible with a two-state unfolding/refolding mechanism for MJ0366. However, the kinetics measured as a function of the temperature show a complex behavior, suggesting a three-state folding mechanism comprising a high-energy intermediate state. The combination of two perturbations, temperature and force, reveals a high-energy species in the folding mechanism of MJ0366 not detected in force-ramp experiments at constant temperature.
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Affiliation(s)
- Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile; Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | | | | | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
| | - Christian A M Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
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44
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Housmans JAJ, Wu G, Schymkowitz J, Rousseau F. A guide to studying protein aggregation. FEBS J 2023; 290:554-583. [PMID: 34862849 DOI: 10.1111/febs.16312] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 12/03/2021] [Indexed: 02/04/2023]
Abstract
Disrupted protein folding or decreased protein stability can lead to the accumulation of (partially) un- or misfolded proteins, which ultimately cause the formation of protein aggregates. Much of the interest in protein aggregation is associated with its involvement in a wide range of human diseases and the challenges it poses for large-scale biopharmaceutical manufacturing and formulation of therapeutic proteins and peptides. On the other hand, protein aggregates can also be functional, as observed in nature, which triggered its use in the development of biomaterials or therapeutics as well as for the improvement of food characteristics. Thus, unmasking the various steps involved in protein aggregation is critical to obtain a better understanding of the underlying mechanism of amyloid formation. This knowledge will allow a more tailored development of diagnostic methods and treatments for amyloid-associated diseases, as well as applications in the fields of new (bio)materials, food technology and therapeutics. However, the complex and dynamic nature of the aggregation process makes the study of protein aggregation challenging. To provide guidance on how to analyse protein aggregation, in this review we summarize the most commonly investigated aspects of protein aggregation with some popular corresponding methods.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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45
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Desai PG, Garidel P, Gbormittah FO, Kamen DE, Mills BJ, Narasimhan CN, Singh S, Stokes ESE, Walsh ER. An Intercompany Perspective on Practical Experiences of Predicting, Optimizing and Analyzing High Concentration Biologic Therapeutic Formulations. J Pharm Sci 2023; 112:359-369. [PMID: 36442683 DOI: 10.1016/j.xphs.2022.11.020] [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: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
Developing high-dose biologic drugs for subcutaneous injection often requires high-concentration formulations and optimizing viscosity, solubility, and stability while overcoming analytical, manufacturing, and administration challenges. To understand industry approaches for developing high-concentration formulations, the Formulation Workstream of the BioPhorum Development Group, an industry-wide consortium, conducted an inter-company collaborative exercise which included several surveys. This collaboration provided an industry perspective, experience, and insight into the practicalities for developing high-concentration biologics. To understand solubility and viscosity, companies desire predictive tools, but experience indicates that these are not reliable and experimental strategies are best. Similarly, most companies prefer accelerated and stress stability studies to in-silico or biophysical-based prediction methods to assess aggregation. In addition, optimization of primary container-closure and devices are pursued to mitigate challenges associated with high viscosity of the formulation. Formulation strategies including excipient selection and application of studies at low concentration to high-concentration formulations are reported. Finally, analytical approaches to high concentration formulations are presented. The survey suggests that although prediction of viscosity, solubility, and long-term stability is desirable, the outcome can be inconsistent and molecule dependent. Significant experimental studies are required to confirm robust product definition as modeling at low protein concentrations will not necessarily extrapolate to high concentration formulations.
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Affiliation(s)
- Preeti G Desai
- Bristol Myers Squibb, Sterile Product Development, 556 Morris Avenue, Summit, NJ 07901, USA
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH Co KG, Innovation Unit, PDB-TIP, 88397 Biberach an der Riss, Germany
| | - Francisca O Gbormittah
- GlaxoSmithKline, Strategic External Development, 1000 Winter Street North, Waltham, MA 02451, USA
| | - Douglas E Kamen
- Regeneron Pharmaceuticals Inc., Formulation Development, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Brittney J Mills
- AbbVie, NBE Drug Product Development, 1 N Waukegan Road, North Chicago, IL 60064, USA
| | | | - Shubhadra Singh
- GlaxoSmithKline R&D, Biopharmaceutical Product Sciences, Collegeville, PA 19426, USA
| | - Elaine S E Stokes
- BioPhorum, The Gridiron Building, 1 Pancras Square, London N1C 4AG UK.
| | - Erika R Walsh
- Merck & Co., Inc., Sterile and Specialty Products, Rahway, NJ, USA
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46
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Aygün C, Kocer S, Danış Ö, Cubuk S, Mutlu O. Heterologous expression, purification, and partial characterisation of the apicoplast protein 3-oxoacyl-[acyl-carrier-protein] reductase from Toxoplasma gondii. Protein Expr Purif 2023; 202:106187. [PMID: 36216219 DOI: 10.1016/j.pep.2022.106187] [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: 07/08/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
Abstract
Recombinant expression and purification of proteins have become a staple of modern drug discovery as it enables more precise in vitro analyses of drug targets, which may help obtain biochemical and biophysical parameters of a known enzyme and even uncover unknown characteristics indicative of novel enzymatic functions. Such information is often necessary to prepare adequate screening assays and drug-discovery experiments in general. Toxoplasma gondii is an obligate protozoan parasite that is a member of the phylum Apicomplexa, can develop several neuro-degenerative symptoms and, in specific cases, certain death for human hosts. Its relict non-photosynthetic plastid, the apicoplast, harbours a unique de novo long-chain fatty acid synthesis pathway of a prokaryotic character, FASII. The FASII pathway shows plasticity and, is essential for many intracellular and membranal components, along with fatty acid uptake via salvaging from the host, therefore, its disruption causes parasite death. TgFabG, a FASII enzyme responsible for a single reduction step in the pathway, was recombinantly expressed, purified and biochemically and biophysically characterised in this study. The bioengineering hurdle of expressing the recombinant gene of a eukaryotic, signal peptide-containing protein in a prokaryotic system was overcome for the apicomplexan enzyme TgFabG, by truncating the N-terminal signal peptide. TgFabG was ultimately recombinantly produced in a plasmid expression vector from its 1131 base pair gene, purified as 260 and 272 amino acid proteins using a hexahistidine (6 × Histag) affinity chromatography and its biochemical (enzyme activity and kinetics) and biophysical characteristics were analysed in vitro.
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Affiliation(s)
- Can Aygün
- Marmara University, Faculty of Arts and Sciences, Department of Biology, 34722, Istanbul, Turkey
| | - Sinem Kocer
- Istanbul Yeni Yüzyıl University, Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, 34010, Istanbul, Turkey
| | - Özkan Danış
- Marmara University, Faculty of Arts and Sciences, Department of Chemistry, 34722, Istanbul, Turkey
| | - Soner Cubuk
- Marmara University, Faculty of Arts and Sciences, Department of Chemistry, 34722, Istanbul, Turkey
| | - Ozal Mutlu
- Marmara University, Faculty of Arts and Sciences, Department of Biology, 34722, Istanbul, Turkey.
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47
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D’Eusanio V, Malferrari D, Marchetti A, Roncaglia F, Tassi L. Waste By-Product of Grape Seed Oil Production: Chemical Characterization for Use as a Food and Feed Supplement. Life (Basel) 2023; 13:life13020326. [PMID: 36836684 PMCID: PMC9958947 DOI: 10.3390/life13020326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Among the waste materials of wine production, grape seeds constitute an important fraction of the pomace, from which the precious edible oil is extracted. The residual mass from oil extraction, the defatted grape seeds (DGS), can be destined for composting or valorized according to the circular economy rules to produce pyrolytic biochar by gasification or pellets for integral energy recovery. Only a small quantity is used for subsequent extraction of polyphenols and tannins. In this study, we performed a chemical characterization of the DGS, by applying spectroscopic techniques (ICP-OES) to determine the metal content, separation techniques (HS-SPME-GC-MS) to evaluate the volatile fraction, and thermal methods of analysis (TGA-MS-EGA) to identify different matrix constituents. Our main goal is to obtain information about the composition of DGS and identify some bioactive compounds constituting the matrix in view of possible future applications. The results suggest that DGS can be further exploited as a dietary supplement, or as an enriching ingredient in foods, for example, in baked goods. Defatted grape seed flour can be used for both human and animal consumption, as it is a source of functional macro- and micronutrients that help in maintaining optimal health and well-being conditions.
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Affiliation(s)
- Veronica D’Eusanio
- Department of Chemical and Geologial Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Correspondence: (V.D.); (L.T.)
| | - Daniele Malferrari
- Department of Chemical and Geologial Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Interdepartmental Research Center BIOGEST-SITEIA, University of Modena and Reggio Emilia, 42124 Reggio Emilia, Italy
| | - Andrea Marchetti
- Department of Chemical and Geologial Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Interdepartmental Research Center BIOGEST-SITEIA, University of Modena and Reggio Emilia, 42124 Reggio Emilia, Italy
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Firenze, Italy
| | - Fabrizio Roncaglia
- Department of Chemical and Geologial Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Firenze, Italy
| | - Lorenzo Tassi
- Department of Chemical and Geologial Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Interdepartmental Research Center BIOGEST-SITEIA, University of Modena and Reggio Emilia, 42124 Reggio Emilia, Italy
- National Interuniversity Consortium of Materials Science and Technology (INSTM), 50121 Firenze, Italy
- Correspondence: (V.D.); (L.T.)
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48
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Ojeda-Galván HJ, Hernández-Arteaga AC, Rodríguez-Aranda MC, Toro-Vazquez JF, Cruz-González N, Ortíz-Chávez S, Comas-García M, Rodríguez AG, Navarro-Contreras HR. Application of Raman spectroscopy for the determination of proteins denaturation and amino acids decomposition temperature. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121941. [PMID: 36208579 DOI: 10.1016/j.saa.2022.121941] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/25/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Raman spectroscopy was employed to study the thermal denaturation of three different proteins, bovine serum albumin (BSA), lysozyme, ovalbumin; and the decomposition temperature of three amino acids, l-glutamine, l-cysteine, and l-alanine, all of them as lyophilized powders. All the Raman bands observed in the spectra obtained were recorded and analyzed at preset heating temperatures. The results obtained for either protein denaturation temperature TD and amino acid decomposition temperatures TM-dc, were compared with those measured by differential scanning calorimetry (DSC). The DSC and Raman results were additionally corroborated with a thermogravimetric analysis (TGA) for the case of proteins. This exercise indicated almost complete coincidence in the determination of these transition temperatures between the three techniques, evidencing the applicability of Raman spectroscopy in the study of denaturation and decomposition temperatures of proteins and amino acids.
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Affiliation(s)
- H J Ojeda-Galván
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a. Sección, CP 78210 San Luis Potosí, SLP, Mexico; Centro de Investigación en Ciencias de la Salud y Biomedicina (CICSaB), Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a. Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - A C Hernández-Arteaga
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a. Sección, CP 78210 San Luis Potosí, SLP, Mexico.
| | - M C Rodríguez-Aranda
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a. Sección, CP 78210 San Luis Potosí, SLP, Mexico.
| | - J F Toro-Vazquez
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, San Luis Potosí 78000, Mexico
| | - N Cruz-González
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a. Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - S Ortíz-Chávez
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a. Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - M Comas-García
- Centro de Investigación en Ciencias de la Salud y Biomedicina (CICSaB), Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a. Sección, CP 78210 San Luis Potosí, SLP, Mexico; Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, San Luis Potosí 78000, Mexico
| | - A G Rodríguez
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a. Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - H R Navarro-Contreras
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a. Sección, CP 78210 San Luis Potosí, SLP, Mexico
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49
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Bucur AI, Poienar M, Bucur RA, Mosoarca C, Banica R. Thermally induced nano-texturing of natural materials: Mytilus galloprovincialis, Mya arenaria and Cerastoderma edule exoskeletons. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2023. [DOI: 10.1007/s43153-022-00297-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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50
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Kasim HBA, Hashim MFB, Yusof AABM, Noodin NHB, Sharudin H, Ismail MHB. Fabrication of Plaque Using Hot Press Method for Recycling Plastic Material. PROCEEDING OF 5TH INTERNATIONAL CONFERENCE ON ADVANCES IN MANUFACTURING AND MATERIALS ENGINEERING 2023:555-561. [DOI: 10.1007/978-981-19-9509-5_73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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