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Terzioglu S, Bittenbinder MA, Slagboom J, van de Velde B, Casewell NR, Kool J. Analytical Size Exclusion Chromatography Coupled with Mass Spectrometry in Parallel with High-Throughput Venomics and Bioassaying for Venom Profiling. Toxins (Basel) 2023; 15:552. [PMID: 37755978 PMCID: PMC10534738 DOI: 10.3390/toxins15090552] [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: 07/11/2023] [Revised: 08/12/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023] Open
Abstract
Modern analytical size exclusion chromatography (SEC) is a suitable technique to separate venom toxin families according to their size characteristics. In this study, a method was developed to separate intact venom toxins from Bungarus multicinctus and Daboia russelii venoms via analytical SEC using volatile, non-salt-containing eluents for post-column mass spectrometry, coagulation bioassaying and high-throughput venomics. Two venoms were used to demonstrate the method developed. While the venom of Bungaurs multicinctus is known to exert anticoagulant effects on plasma, in this study, we showed the existence of both procoagulant toxins and anticoagulant toxins. For Daboia russelii venom, the method revealed characteristic procoagulant effects, with a 90 kDa mass toxin detected and matched with the Factor X-activating procoagulant heterotrimeric glycoprotein named RVV-X. The strong procoagulant effects for this toxin show that it was most likely eluted from size exclusion chromatography non-denatured. In conclusion, the separation of snake venom by size gave the opportunity to separate some specific toxin families from each other non-denatured, test these for functional bioactivities, detect the eluting mass on-line via mass spectrometry and identify the eluted toxins using high-throughput venomics.
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Affiliation(s)
- Sedef Terzioglu
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Mátyás A. Bittenbinder
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
| | - Julien Slagboom
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Bas van de Velde
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Nicholas R. Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Jeroen Kool
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
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2
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Bittenbinder MA, Capinha L, Da Costa Pereira D, Slagboom J, van de Velde B, Casewell NR, Jennings P, Kool J, Vonk FJ. Development of a high-throughput in vitro screening method for the assessment of cell-damaging activities of snake venoms. PLoS Negl Trop Dis 2023; 17:e0011564. [PMID: 37590328 PMCID: PMC10465002 DOI: 10.1371/journal.pntd.0011564] [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: 10/27/2022] [Revised: 08/29/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
Snakebite envenoming is a globally important public health issue that has devastating consequences on human health and well-being, with annual mortality rates between 81,000 and 138,000. Snake venoms may cause different pathological effects by altering normal physiological processes such as nervous transfer and blood coagulation. In addition, snake venoms can cause severe (local) tissue damage that may result in life-long morbidities, with current estimates pointing towards an additional 450,000 individuals that suffer from permanent disabilities such as amputations, contractions and blindness. Despite such high morbidity rates, research to date has been mainly focusing on neurotoxic and haemotoxic effects of snake venoms and considerably less on venom-induced tissue damage. The molecular mechanisms underlaying this pathology include membrane disruption and extracellular matrix degradation. This research describes methods used to study the (molecular) mechanisms underlaying venom-induced cell- and tissue damage. A selection of cellular bioassays and fluorescent microscopy were used to study cell-damaging activities of snake venoms in multi-well plates, using both crude and fractionated venoms. A panel of 10 representative medically relevant snake species was used, which cover a large part of the geographical regions most heavily affected by snakebite. The study comprises both morphological data as well as quantitative data on cell metabolism and viability, which were measured over time. Based on this data, a distinction could be made in the ways by which viper and elapid venoms exert their effects on cells. We further made an effort to characterise the bioactive compounds causing these effects, using a combination of liquid chromatography methods followed by bioassaying and protein identification using proteomics. The outcomes of this study might prove valuable for better understanding venom-induced cell- and tissue-damaging pathologies and could be used in the process of developing and improving snakebite treatments.
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Affiliation(s)
- Matyas A. Bittenbinder
- Naturalis Biodiversity Center, Leiden, The Netherlands
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
| | - Liliana Capinha
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Daniel Da Costa Pereira
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Julien Slagboom
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
| | - Bas van de Velde
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
| | - Nicholas R. Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Paul Jennings
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jeroen Kool
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
| | - Freek J. Vonk
- Naturalis Biodiversity Center, Leiden, The Netherlands
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
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3
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Wachtel E, Bittenbinder MA, van de Velde B, Slagboom J, de Monts de Savasse A, Alonso LL, Casewell NR, Vonk FJ, Kool J. Application of an Extracellular Matrix-Mimicking Fluorescent Polymer for the Detection of Proteolytic Venom Toxins. Toxins (Basel) 2023; 15:toxins15040294. [PMID: 37104232 PMCID: PMC10143632 DOI: 10.3390/toxins15040294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/28/2023] Open
Abstract
The cytotoxicity caused by snake venoms is a serious medical problem that greatly contributes to the morbidity observed in snakebite patients. The cytotoxic components found in snake venoms belong to a variety of toxin classes and may cause cytotoxic effects by targeting a range of molecular structures, including cellular membranes, the extracellular matrix (ECM) and the cytoskeleton. Here, we present a high-throughput assay (384-well plate) that monitors ECM degradation by snake venom toxins via the application of fluorescent versions of model ECM substrates, specifically gelatin and collagen type I. Both crude venoms and fractionated toxins of a selection of medically relevant viperid and elapid species, separated via size-exclusion chromatography, were studied using the self-quenching, fluorescently labelled ECM-polymer substrates. The viperid venoms showed significantly higher proteolytic degradation when compared to elapid venoms, although the venoms with higher snake venom metalloproteinase content did not necessarily exhibit stronger substrate degradation than those with a lower one. Gelatin was generally more readily cleaved than collagen type I. In the viperid venoms, which were subjected to fractionation by SEC, two (B. jararaca and C. rhodostoma, respectively) or three (E. ocellatus) active proteases were identified. Therefore, the assay allows the study of proteolytic activity towards the ECM in vitro for crude and fractionated venoms.
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Affiliation(s)
- Eric Wachtel
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Matyas A Bittenbinder
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Bas van de Velde
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Julien Slagboom
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Axel de Monts de Savasse
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Luis L Alonso
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Nicholas R Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Freek J Vonk
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Jeroen Kool
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
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4
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Rapid Biomarker-Based Diagnosis of Fibromyalgia Syndrome and Related Rheumatologic Disorders by Portable FT-IR Spectroscopic Techniques. Biomedicines 2023; 11:biomedicines11030712. [PMID: 36979691 PMCID: PMC10044908 DOI: 10.3390/biomedicines11030712] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
Fibromyalgia syndrome (FM), one of the most common illnesses that cause chronic widespread pain, continues to present significant diagnostic challenges. The objective of this study was to develop a rapid vibrational biomarker-based method for diagnosing fibromyalgia syndrome and related rheumatologic disorders (systemic lupus erythematosus (SLE), osteoarthritis (OA) and rheumatoid arthritis (RA)) through portable FT-IR techniques. Bloodspot samples were collected from patients diagnosed with FM (n = 122) and related rheumatologic disorders (n = 70), including SLE (n = 17), RA (n = 43), and OA (n = 10), and stored in conventional protein saver bloodspot cards. The blood samples were prepared by four different methods (blood aliquots, protein-precipitated extraction, and non-washed and water-washed semi-permeable membrane filtration extractions), and spectral data were collected with a portable FT-IR spectrometer. Pattern recognition analysis, OPLS-DA, was able to identify the signature profile and classify the spectra into corresponding classes (Rcv > 0.93) with excellent sensitivity and specificity. Peptide backbones and aromatic amino acids were predominant for the differentiation and might serve as candidate biomarkers for syndromes such as FM. This research evaluated the feasibility of portable FT-IR combined with chemometrics as an accurate and high-throughput tool for distinct spectral signatures of biomarkers related to the human syndrome (FM), which could allow for real-time and in-clinic diagnostics of FM.
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5
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Yu H, Kim S, Chang PS. Lipase-catalyzed production of pyridoxine monolaurate in solvent-free bioreactor system. Food Chem 2023; 399:133949. [DOI: 10.1016/j.foodchem.2022.133949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022]
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6
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Yang Y, Yin Y, Tang X, Xia Y, Zhang J, Yan C, Zhang W, Zhang H, Han TL. Evaluating Different Extraction Approaches for GC-MS Based Metabolomics Analysis of the Giant Pandas' Fur. TOXICS 2022; 10:688. [PMID: 36422896 PMCID: PMC9696619 DOI: 10.3390/toxics10110688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/04/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Giant pandas in zoo captivity are situated in residential areas, where environmental pollutants and anthropogenic factors have an impact on their health. Hair metabolomics has been applied in numerous environmental toxicological studies. Therefore, the panda fur metabolome could be a reliable approach to reflect endogenous and exogenous metabolic changes related to environmental exposure. However, there is no established extraction protocol to study the fur metabolome of pandas. The aim of this research was to optimize the extraction of panda fur metabolome for high-throughput metabolomics analysis using gas chromatography-mass spectrometry. Fur samples were collected from five pandas. Eight different extraction methods were investigated and evaluated for their reproducibility, metabolite coverage, and extraction efficiency, particularly in relation to the biochemical compound classes such as amino acids, tricarboxylic acid cycle derivatives, fatty acids, and secondary metabolites. Our results demonstrated that HCl + ACN were the superior extraction solvents for amino acid and secondary metabolite extraction, and NaOH + MeOH was ideal for fatty acid extraction. Interestingly, the metabolomic analysis of panda fur was capable of discriminating the longitudinal metabolite profile between black and white furs. These extraction protocols can be used in future study protocols for the analysis of the fur metabolome in pandas.
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Affiliation(s)
- Yang Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Ministry of Education of China International Collaborative Joint Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing 400000, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing 400000, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400000, China
| | | | - Xianglan Tang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Yinyin Xia
- School of Public Health and Management, Chongqing Medical University, Chongqing 400000, China
| | - Jinya Zhang
- School of Clinical Medicine, Chongqing Medical University, Chongqing 400000, China
| | - Chun Yan
- School of Clinical Medicine, Chongqing Medical University, Chongqing 400000, China
| | - Weixuan Zhang
- School of Clinical Medicine, Chongqing Medical University, Chongqing 400000, China
| | - Hua Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Ministry of Education of China International Collaborative Joint Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing 400000, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing 400000, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400000, China
| | - Ting-Li Han
- Ministry of Education of China International Collaborative Joint Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing 400000, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing 400000, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400000, China
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
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Optimization and Identification of Single Mutation in Hemoglobin Variants with 2,2,2 Trifluoroethanol Modified Digestion Method and Nano-LC Coupled MALDI MS/MS. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196357. [PMID: 36234894 PMCID: PMC9572498 DOI: 10.3390/molecules27196357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 12/30/2022]
Abstract
Background: Hemoglobin (Hb) variants arise due to point mutations in globin chains and their pathological treatments rely heavily on the identification of the nature and location of the mutation in the globin chains. Traditional methods for diagnosis such as HPLC and electrophoresis have their own limitations. Therefore, the present study aims to develop and optimize a specific method of sample processing that could lead to improved sequence coverage and analysis of Hb variants by nano LC-MALDI MS/MS. Methods: In our study, we primarily standardized various sample processing methods such as conventional digestion with trypsin followed by 10% acetonitrile treatment, digestion with multiple proteases like trypsin, Glu-C, Lys-C, and trypsin digestion subsequent to 2,2,2 trifluoroethanol (TFE) treatment. Finally, the peptides were identified by LC-MALDI MS/MS. All of these sample processing steps were primarily tested with recombinant Hb samples. After initial optimization, we found that the TFE method was the most suitable one and the efficiency of this method was applied in Hb variant identification based on high sequence coverage. Results: We developed and optimized a method using an organic solvent TFE and heat denaturation prior to digestion, resulting in 100% sequence coverage in the β-chains and 95% sequence coverage in the α-chains, which further helped in the identification of Hb mutations. A Hb variant protein sequence database was created to specify the search and reduce the search time. Conclusion: All of the mutations were identified using a bottom-up non-target approach. Therefore, a sensitive, robust and reproducible method was developed to identify single substitution mutations in the Hb variants from the sequence of the entire globin chains. Biological Significance: Over 330,000 infants are born annually with hemoglobinopathies and it is the major cause of morbidity and mortality in early childhood. Hb variants generally arise due to point mutation in the globin chains. There is high sequence homology between normal Hb and Hb variant chains. Due to this high homology between the two forms, identification of variants by mass spectrometry is very difficult and requires the full sequence coverage of α- and β-chains. As such, there is a need for a suitable method that provides 100% sequence coverage of globin chains for variant analysis by mass spectrometry. Our study provides a simple, robust, and reproducible method that is suitable for LC-MALDI and provides nearly complete sequence coverage in the globin chains. This method may be used in the near future in routine diagnosis for Hb variant analysis.
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Preparation of Antihypertensive Drugs in Biological Matrix with Solvent Front Position Extraction for LC–MS/MS Analysis. Molecules 2021; 27:molecules27010205. [PMID: 35011437 PMCID: PMC8746826 DOI: 10.3390/molecules27010205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Solvent front position extraction procedure was used to prepare biological samples containing selected antihypertensive drugs (ramipril, lercanidipine, indapamide, valsartan, hydrochlorothiazide, perindopril, and nebivolol). Substances separated from the biological matrix components (bovine serum albumin) were quantified by means of liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Sample preparation process was performed with the use of a prototype horizontal chamber with a moving pipette driven by a 3D printer mechanism enabling a controlled eluent flow velocity. Application of this device was advantageous for simultaneous preparation of several samples for further quantitative analysis, with a synchronized reduction of manual operations and solvent consumption. Quantitative results obtained for the majority of the investigated antihypertensive drugs in a complex biological matrix were satisfactory. The values of the %RSD were around 5% for six of the seven substances (with the exception of indapamide). The method exhibits a suitable accuracy (the relative error percentage was below 10% for most drugs). The values of LOD and LOQ were in the range of 1.19 µg/L–8.53 µg/L and 3.61 µg/L–25.8 µg/L, respectively.
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Afzal Shoushtari B, Rahbar Shahrouzi J, Pazuki G, Shahriari S, Hadidi N. Separation of glatiramer acetate and its constituent amino acids using aqueous two-phase systems composed of maltodextrin and acetonitrile. J IND ENG CHEM 2021. [DOI: 10.1016/j.jiec.2021.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Sharma N, Leung IKH. Characterisation and optimisation of a novel laccase from Sulfitobacter indolifex for the decolourisation of organic dyes. Int J Biol Macromol 2021; 190:574-584. [PMID: 34506861 DOI: 10.1016/j.ijbiomac.2021.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/19/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Laccases are multi‑copper oxidases that possess the potential for industrial wastewater treatments. In this study, a putative laccase from Sulfitobacter indolifex was recombinantly produced and characterised. The enzyme was found to be stable and active at low to ambient temperature and across a range of pH conditions. The ability of the putative bacterial laccase to catalyse the decolourisation of seven common industrial dyes was also examined. Our results showed that the putative laccase could efficiently decolourise Indigo Carmine, Coomassie Brilliant Blue R-250, Congo Red, Malachite Green and Alizarin in the presence of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) as a redox mediator. Furthermore, the use of enzyme immobilisation technology to improve the operational stability and reusability of the putative laccase was also investigated. We found that immobilising the enzyme through the cross-linked enzyme aggregate method significantly improved its tolerance towards extreme pH as well as the presence of organic solvents. This work expands the arsenal of bacterial laccases available for the bioremediation of dye-containing wastewater.
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Affiliation(s)
- Nabangshu Sharma
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia; Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
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11
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Kang MS, Kong TWS, Khoo JYX, Loh TP. Recent developments in chemical conjugation strategies targeting native amino acids in proteins and their applications in antibody-drug conjugates. Chem Sci 2021; 12:13613-13647. [PMID: 34760149 PMCID: PMC8549674 DOI: 10.1039/d1sc02973h] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Many fields in chemical biology and synthetic biology require effective bioconjugation methods to achieve their desired functions and activities. Among such biomolecule conjugates, antibody-drug conjugates (ADCs) need a linker that provides a stable linkage between cytotoxic drugs and antibodies, whilst conjugating in a biologically benign, fast and selective fashion. This review focuses on how the development of novel organic synthesis can solve the problems of traditional linker technology. The review shall introduce and analyse the current developments in the modification of native amino acids on peptides or proteins and their applicability to ADC linker. Thereafter, the review shall discuss in detail each endogenous amino acid's intrinsic reactivity and selectivity aspects, and address the research effort to construct an ADC using each conjugation method.
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Affiliation(s)
- Min Sun Kang
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Theresa Wai See Kong
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Joycelyn Yi Xin Khoo
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Teck-Peng Loh
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
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12
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Sharma N, Leung IK. Novel Thermophilic Bacterial Laccase for the Degradation of Aromatic Organic Pollutants. Front Chem 2021; 9:711345. [PMID: 34746090 PMCID: PMC8564365 DOI: 10.3389/fchem.2021.711345] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/30/2021] [Indexed: 12/07/2022] Open
Abstract
We identified a putative laccase from the thermophilic bacterium Geobacillus yumthangensis. The putative laccase was produced recombinantly and its ability to catalyse the degradation of aromatic organic pollutants was investigated. The putative laccase exhibits broad pH and temperature stability, and, notably, it could catalyse the degradation of organic dyes as well as toxic pollutants including bisphenol A, guaiacol and phenol with a redox mediator. Our work further demonstrates the potential of using oxidative enzymes to break down toxic chemicals that possess major threats to human health and the environment.
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Affiliation(s)
- Nabangshu Sharma
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Ivanhoe K.H. Leung
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
- Centre for Green Chemical Science, The University of Auckland, Auckland, New Zealand
- School of Chemistry, The University of Melbourne, Parkville, VIC, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
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13
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Wang X, Chen X, Nonin-Lecomte S, Bouaziz S. Acetonitrile allows indirect replacement of nondeuterated lipid detergents by deuterated lipid detergents for the nuclear magnetic resonance study of detergent-soluble proteins. Protein Sci 2021; 30:2324-2332. [PMID: 34462977 DOI: 10.1002/pro.4174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 02/06/2023]
Abstract
Detergent-soluble proteins (DSPs) are commonly dissolved in lipid buffers for NMR experiments, but the huge lipid proton signal prevents recording of high-quality spectra. The use of costly deuterated lipids is thus required to replace nondeuterated ones. With conventional methods, detergents like dodecylphosphocholine (DPC) cannot be fully exchanged due to their high binding affinity to hydrophobic proteins. We propose an original and simple protocol which combines the use of acetonitrile, dialysis and lyophilization to disrupt the binding of lipids to the protein and allow their indirect replacement by their deuterated equivalents, while maintaining the native structure of the protein. Moreover, by this protocol, the detergent-to-protein molar ratio can be controlled as it challenges the protein structure. This protocol was applied to solubilize the Vpx protein that was followed upon addition of DPC-d38 by 1 H-15 N SOFAST-HMQC spectra and the best detergent-to-DSPs molar ratio was obtained for structural studies.
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Affiliation(s)
- Xiao Wang
- CiTCoM, CNRS, UMR 8038, Université de Paris, Paris, France
| | - Xiaowei Chen
- CiTCoM, CNRS, UMR 8038, Université de Paris, Paris, France
| | | | - Serge Bouaziz
- CiTCoM, CNRS, UMR 8038, Université de Paris, Paris, France
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14
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Meyer RM, Berger L, Nerkamp J, Scheler S, Nehring S, Friess W. Identification of monoclonal antibody variants involved in aggregate formation - Part 2: Hydrophobicity variants. Eur J Pharm Biopharm 2021; 160:134-142. [PMID: 33524536 DOI: 10.1016/j.ejpb.2021.01.006] [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: 10/26/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 11/29/2022]
Abstract
Monoclonal antibodies (mAbs) are valuable tools both in therapy and in diagnostic. Their tendency to aggregate is a serious concern. Since a mAb drug substance (DS) is composed of different variants, it is important for manufacturers to know the behavior and stability not only of the mAb as a whole, but also of the variants contained in the product. We present a method to separate hydrophobicity variants of a mAb and subsequently analyzed these variants for stability and aggregation propensity. We identified a potentially aggregation prone hydrophilic variant which is interrelated with another previously identified aggregation prone acidic charge variant. Additionally, we assessed the risk posed by the aggregation prone variant to the DS by spiking hydrophobicity variants into DS and did not observe an enhanced aggregation propensity. Thus we present an approach to separate, characterize and analyze the criticality of aggregation prone variants in protein DS which is a step forward to further assure drug safety.
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Affiliation(s)
- Robina M Meyer
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, University of Munich, Butenandtstr. 5, 81377 Munich, Germany
| | - Lukas Berger
- Sandoz Biopharmaceutics, Biochemiestr. 10, 6336 Langkampfen, Austria
| | - Joerg Nerkamp
- Sandoz Biopharmaceutics, Biochemiestr. 10, 6336 Langkampfen, Austria
| | - Stefan Scheler
- Sandoz Biopharmaceutics, Biochemiestr. 10, 6336 Langkampfen, Austria
| | - Sebastian Nehring
- Sandoz Biopharmaceutics, Biochemiestr. 10, 6336 Langkampfen, Austria
| | - Wolfgang Friess
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, University of Munich, Butenandtstr. 5, 81377 Munich, Germany.
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15
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Development of a Pass-through SPE Cartridge for the Rapid Determination of Fipronil and Its Metabolites in Chicken Eggs by LC-MS/MS. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-020-01902-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Wong S, Kemp JA, Shim MS, Kwon YJ. Solvent-driven, self-assembled acid-responsive poly(ketalized serine)/siRNA complexes for RNA interference. Biomater Sci 2020; 8:6718-6729. [PMID: 33111729 DOI: 10.1039/d0bm01478h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Advances in bionanotechnology aim to develop smart nucleic acid delivery carriers with stimuli-responsive features to overcome challenges such as non-biodegradability, rapid clearance, immune response, and reaching intracellular targets. Peptide-based nanomaterials have become widely used in the field of gene and drug delivery due to their structural versatility and biomimetic properties. Particularly, polypeptide gene vectors that respond to biological stimuli, such as acidic intracellular environments, have promising applications in mediating efficient endosomal escape and drug release. Unfortunately, synthesis strategies for efficient polymerization of acid-labile peptides have been limited due to conditions that fail to preserve acid-degradable functional groups. Stable urethane derivatives of the acid-labile amino acid ketalized serine (kSer) were synthesized and polymerized to a high molecular weight under permissive conditions independent of elevated temperature, restrictive solvents, or an inert atmosphere. A new formulation strategy utilizing solvent-driven self-assembly of poly(kSer) peptides with small interfering RNA (siRNA) was developed, and the resulting poly(kSer)/siRNA complexes were further cross-linked for reinforced stability under physiological conditions. The complexes were highly monodisperse and precisely spherical in morphology, which has significant clinical implications in definitive biodistribution, cellular internalization, and intracellular trafficking patterns. Self-assembled, cross-linked poly(kSer)/siRNA complexes demonstrated efficient nucleic acid encapsulation, internalization, endosomal escape, and acid-triggered cargo release, tackling multiple hurdles in siRNA delivery. The acid-responsive polypeptides and solvent-driven self-assembly strategies demonstrated in this study could be applicable to developing other efficient and safe delivery systems for gene and drug delivery.
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Affiliation(s)
- Shirley Wong
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA.
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17
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Bladek T, Szymanek-Bany I, Posyniak A. Determination of Polypeptide Antibiotic Residues in Food of Animal Origin by Ultra-High-Performance Liquid Chromatography-Tandem Mass Spectrometry. Molecules 2020; 25:molecules25143261. [PMID: 32708914 PMCID: PMC7396995 DOI: 10.3390/molecules25143261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 11/26/2022] Open
Abstract
A novel UHPLC-MS/MS method for the determination of polypeptide antibiotic residues in animal muscle, milk, and eggs was developed and validated. Bacitracin A, colistin A, colistin B, polymyxin B1, and polymyxin B2 were extracted from the samples with a mixture of acetonitrile/water/ammonia solution 25%, 80/10/10 (v/v/v), and put through further evaporation, reconstitution, and filtration steps. The chromatographic separation was performed on a C18 column in gradient elution mode. Mass spectral acquisitions were performed in selective multiple reaction monitoring mode by a triple quadrupole mass spectrometer. The method was validated according to the criteria of Commission Decision 2002/657/EC. The method quantifies polypeptides in a linear range from 10 to 1000 μg kg−1, where the lowest concentration on the calibration curve refers to the limit of quantification (LOQ). The recoveries ranged from 70 to 99%, the repeatability was below 13%, and within-laboratory reproducibility was lower than 15%. The decision limit (CCα) and detection capability (CCβ) values were calculated, and ruggedness and stability studies were performed, to fulfill the criteria for confirmatory methods. Moreover, the developed method may also be used for screening purposes by its labor efficiency.
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18
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Chen Z, Zhou R, Yin H, Yuan S. Determination and correlation of temperature and pHvalue dependent solubility of dl‐methionine. AIChE J 2020. [DOI: 10.1002/aic.16270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zhirong Chen
- College of Chemical and Biological EngineeringZhejiang University Hangzhou China
| | - Rongfan Zhou
- College of Chemical and Biological EngineeringZhejiang University Hangzhou China
| | - Hong Yin
- College of Chemical and Biological EngineeringZhejiang University Hangzhou China
| | - Shenfeng Yuan
- College of Chemical and Biological EngineeringZhejiang University Hangzhou China
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19
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Maser TL, Honarvar E, Venter AR. Delayed Desorption Improves Protein Analysis by Desorption Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:803-811. [PMID: 32157888 DOI: 10.1021/jasms.9b00047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein analysis by desorption electrospray ionization mass spectrometry (DESI-MS) is limited and often accompanied by a mass-dependent loss in sensitivity as protein molecular weight increases. Previously, incomplete dissolution was identified as a potential contributing factor to this limitation for larger proteins. Here, we developed a unique two-step configuration in which a prewetting solvent is applied to the sample surface proximal to DESI analysis by a wetting quill to increase dissolution time and the detection of larger proteins. After optimizing the system with a mixture of proteins containing cytochrome c, myoglobin, and chymotripsinogen, we demonstrate the ability of delayed desorption to improve the analysis of larger proteins such as bovine serum albumin. Albumin and other serum proteins, including even larger ones, were also detected directly from diluted goat serum. An additional feature of this technique is the ability to deliver multiple solvents with potential synergistic or cooperative effects. For example, when using acetonitrile solutions of formic acid and ammonium bicarbonate as the prewetting and DESI spray solvent, respectively, the intensity of chymotrypsinogen improved dramatically compared to controls but less so for smaller proteins such as myoglobin and cytochrome c. Adduct removal was also observed for all proteins. These early results demonstrate the ability of this two-step technique for the use of multiple additives and increased dissolution times compared to standard DESI-MS experiments.
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Affiliation(s)
- Tara L Maser
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
| | - Elahe Honarvar
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
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20
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Structural Characterization of the S-glycosylated Bacteriocin ASM1 from Lactobacillus plantarum. MAGNETOCHEMISTRY 2020. [DOI: 10.3390/magnetochemistry6010016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In order to protect their environmental niche, most bacteria secret antimicrobial substances designed to target specific bacterial strains that are often closely related to the producer strain. Bacteriocins, small, ribosomally synthesised antimicrobial peptides, comprise a class of such substances and can either inhibit (bacteriostatic) or kill (bactericidal) target cells. Glycocins are a class of bacteriocin that are post-translationally modified by one or more carbohydrate moieties that are either β-O-linked to either a serine or threonine and/or β-S-linked to a cysteine. The solution nuclear magnetic resonance structure (NMR) of the glycocin ASM1 (produced by Lactobacillus plantarum A-1), an orthologue of GccF, has been determined. In both structures, the disulfide bonds are essential for activity and restrict the mobility of the N-acetyl-glucosamine (GlcNAc) attached to Ser-18 (O-linked), compared to the much more flexible GlcNAc moiety on Cys-43 (S-linked). Interestingly, despite 88% sequence identity, the helical structure of ASM1 is less pronounced which appears to be consistent with the far ultra-violet circular dichroism (UV CD) spectra.
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21
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Hirano A, Nagatoishi S, Wada M, Tsumoto K, Maluf KN, Arakawa T. Technical Capabilities and Limitations of Optical Spectroscopy and Calorimetry Using Water-Miscible Solvents: The Case of Dimethyl Sulfoxide, Acetonitrile, and 1,4-Dioxane. J Pharm Sci 2019; 109:524-531. [PMID: 31682831 DOI: 10.1016/j.xphs.2019.10.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/22/2019] [Accepted: 10/29/2019] [Indexed: 01/09/2023]
Abstract
In drug development, water-miscible solvents are commonly used to dissolve drug substances. Typical routine procedures in drug development include dilution of the stock drug solution into an aqueous solution containing target macromolecules for drug binding assays. However, water-miscible solvents impose some technical limitations on the assays on account of their light absorption and heat capacity. Here, we examined the effects of the dilution of 3 water-miscible solvents, that is, dimethyl sulfoxide, acetonitrile, and 1,4-dioxane, on the baseline stability and signal/noise ratio in circular dichroism spectroscopy, isothermal titration calorimetry, and differential scanning calorimetry. Dimethyl sulfoxide and 1,4-dioxane affect the signal/noise ratio of circular dichroism spectra at typically used concentrations due to their light absorbance. The water-miscible solvents generate interfering signals in the isothermal titration calorimetry due to their mixing heat. They show negative or positive slope in the differential scanning calorimetry. Such interfering effects of the solvents are reduced by appropriate dilution according to the analytical techniques. Because the water-miscible solvents have solubilization capacity for alkyl chain moieties and aromatic moieties of chemicals, drug substances containing these moieties can be dissolved into the solvents and then subjected to the analyses to examine their interactions with target proteins after appropriate dilution of the drug solutions.
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Affiliation(s)
- Atsushi Hirano
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan.
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Momoyo Wada
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Karl N Maluf
- Alliance Protein Laboratories, Division of KBI Biopharma, San Diego, California 92121
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, Division of KBI Biopharma, San Diego, California 92121
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22
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Artur MAS, Rienstra J, Dennis TJ, Farrant JM, Ligterink W, Hilhorst H. Structural Plasticity of Intrinsically Disordered LEA Proteins from Xerophyta schlechteri Provides Protection In Vitro and In Vivo. FRONTIERS IN PLANT SCIENCE 2019; 10:1272. [PMID: 31681372 PMCID: PMC6798065 DOI: 10.3389/fpls.2019.01272] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/11/2019] [Indexed: 05/27/2023]
Abstract
Late embryogenesis abundant (LEA) proteins are essential to the ability of resurrection plants and orthodox seeds to protect the subcellular milieu against irreversible damage associated with desiccation. In this work, we investigated the structure and function of six LEA proteins expressed during desiccation in the monocot resurrection species Xerophyta schlechteri (XsLEAs). In silico analyses suggested that XsLEAs are hydrophilic proteins with variable intrinsically disordered protein (IDP) properties. Circular dichroism (CD) analysis indicated that these proteins are mostly unstructured in water but acquire secondary structure in hydrophobic solution, suggesting that structural dynamics may play a role in their function in the subcellular environment. The protective property of XsLEAs was demonstrated by their ability to preserve the activity of the enzyme lactate dehydrogenase (LDH) against desiccation, heat and oxidative stress, as well as growth of Escherichia coli upon exposure to osmotic and salt stress. Subcellular localization analysis indicated that XsLEA recombinant proteins are differentially distributed in the cytoplasm, membranes and nucleus of Nicotiana benthamiana leaves. Interestingly, a LEA_1 family protein (XsLEA1-8), showing the highest disorder-to-order propensity and protective ability in vitro and in vivo, was also able to enhance salt and drought stress tolerance in Arabidopsis thaliana. Together, our results suggest that the structural plasticity of XsLEAs is essential for their protective activity to avoid damage of various subcellular components caused by water deficit stress. XsLEA1-8 constitutes a potential model protein for engineering structural stability in vitro and improvement of water-deficit stress tolerance in plants.
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Affiliation(s)
| | - Juriaan Rienstra
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - Timothy J. Dennis
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Jill M. Farrant
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Wilco Ligterink
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - Henk Hilhorst
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
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23
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Wiezel GA, Rustiguel JK, Morgenstern D, Zoccal KF, Faccioli LH, Nonato MC, Ueberheide B, Arantes EC. Insights into the structure, function and stability of bordonein-L, the first L-amino acid oxidase from Crotalus durissus terrificus snake venom. Biochimie 2019; 163:33-49. [DOI: 10.1016/j.biochi.2019.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/06/2019] [Indexed: 01/18/2023]
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Kurokawa N, Kishimoto T, Tanaka K, Kondo J, Takahashi N, Miura Y. New approach to evaluating the effects of a drug on protein complexes with quantitative proteomics, using the SILAC method and bioinformatic approach. Biosci Biotechnol Biochem 2019; 83:2034-2048. [PMID: 31282289 DOI: 10.1080/09168451.2019.1637244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Protein-protein interactions (PPIs) lead the formation of protein complexes that perform biochemical reactions that maintain the living state of the living cell. Although therapeutic drugs should influence the formation of protein complexes in addition to PPI network, the methodology analyzing such influences remain to be developed. Here, we demonstrate that a new approach combining HPLC (high performance liquid chromatography) for separating protein complexes, and the SILAC (stable isotope labeling using amino acids in cell culture) method for relative protein quantification, enable us to identify the protein complexes influenced by a drug. We applied this approach to the analysis of thalidomide action on HepG2 cells, assessed the identified proteins by clustering data analyses, and assigned 135 novel protein complexes affected by the drug. We propose that this approach is applicable to elucidating the mechanisms of actions of other therapeutic drugs on the PPI network, and the formation of protein complexes.
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Affiliation(s)
- Natsuki Kurokawa
- Graduate School of Agriculture, Tokyo University of Agriculture & Technology , Fuchu-shi, Tokyo , Japan.,Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , Chuo-ku , Japan
| | - Taro Kishimoto
- Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , Chuo-ku , Japan
| | - Kohei Tanaka
- Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , Chuo-ku , Japan
| | - Jun Kondo
- Innovative Research Division, Mitsubishi Tanabe Pharma Corporation , Chuo-ku , Japan
| | - Nobuhiro Takahashi
- Graduate School of Agriculture, Tokyo University of Agriculture & Technology , Fuchu-shi, Tokyo , Japan
| | - Yutaka Miura
- Graduate School of Agriculture, Tokyo University of Agriculture & Technology , Fuchu-shi, Tokyo , Japan
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25
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Schoubben A, Vivani R, Paolantoni M, Perinelli DR, Gioiello A, Macchiarulo A, Ricci M. D-leucine microparticles as an excipient to improve the aerosolization performances of dry powders for inhalation. Eur J Pharm Sci 2019; 130:54-64. [DOI: 10.1016/j.ejps.2019.01.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/21/2019] [Indexed: 11/25/2022]
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26
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Cordeiro FA, Coutinho BM, Wiezel GA, Bordon KDCF, Bregge-Silva C, Rosa-Garzon NG, Cabral H, Ueberheide B, Arantes EC. Purification and enzymatic characterization of a novel metalloprotease from Lachesis muta rhombeata snake venom. J Venom Anim Toxins Incl Trop Dis 2018; 24:32. [PMID: 30498508 PMCID: PMC6251203 DOI: 10.1186/s40409-018-0171-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/01/2018] [Indexed: 11/25/2022] Open
Abstract
Background Lachesis muta rhombeata (Lmr) is the largest venomous snake in Latin America and its venom contains mainly enzymatic components, such as serine and metalloproteases, L-amino acid oxidase and phospholipases A2. Metalloproteases comprise a large group of zinc-dependent proteases that cleave basement membrane components such as fibronectin, laminin and collagen type IV. These enzymes are responsible for local and systemic changes, including haemorrhage, myonecrosis and inflammation. This study aimed the isolation and enzymatic characterization of the first metalloprotease (Lmr-MP) from Lmr venom (LmrV). Methods and results Lmr-MP was purified through two chromatographic steps and submitted to enzymatic characterization. It showed proteolytic activity on azocasein with maximum activity at pH 7.0–9.0. It was inhibited by EDTA (a metal chelator that removes zinc, which is essential for enzymatic activity) and no effect was observed with PMSF, iodoacetic acid or pepstatin (inhibitors of serine, cysteine and aspartyl proteases, respectively). Ca2+, Mg2+ and Ba2+ ions increased its activity, while Al3+, Cu2+, Ni2+ and Zn2+ inhibited it. Additionally, ZnCl2 showed a dose dependent inhibition of the enzyme. Lmr-MP activity was also evaluated upon chromogenic substrates for plasma kallikrein (S-2302), plasmin and streptokinase-activated plasminogen (S-2251) and Factor Xa (S-2222) showing the highest activity on S-2302. The activity in different solutions (5 mM or 50 mM ammonium bicarbonate, pH 7.8; 0.1% trifluoroacetic acid + 50% acetonitrile; phosphate buffer saline, pH 7.4; 50 mM sodium acetate, pH 4.0 or ammonium acetate pH 4.5) was also evaluated and the results showed that its activity was abolished at acidic pHs. Its molecular mass (22,858 Da) was determined by MALDI-TOF and about 90% of its primary structure was verified by high-resolution mass spectrometry using HCD and ETD fragmentations and database search against the sequence of closely related species. It is a novel enzyme which shared high identity with other snake venom metalloproteases (svMPs) belonging to the P-I group. Conclusion The purification procedure achieved a novel pure highly active metalloprotease from LmrV. This new molecule can help to understand the metalloproteases mechanisms of action, the Lachesis envenoming, as well as to open new perspectives for its use as therapeutic tools.
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Affiliation(s)
- Francielle Almeida Cordeiro
- 1Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café s/n°, Monte Alegre, Ribeirão Preto, SP 14040-903 Brazil
| | - Bárbara Marques Coutinho
- 1Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café s/n°, Monte Alegre, Ribeirão Preto, SP 14040-903 Brazil
| | - Gisele Adriano Wiezel
- 1Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café s/n°, Monte Alegre, Ribeirão Preto, SP 14040-903 Brazil
| | - Karla de Castro Figueiredo Bordon
- 1Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café s/n°, Monte Alegre, Ribeirão Preto, SP 14040-903 Brazil
| | | | - Nathalia Gonsales Rosa-Garzon
- 3Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP Brazil
| | - Hamilton Cabral
- 3Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP Brazil
| | - Beatrix Ueberheide
- 4Proteomics Resource Center, New York University Langone Medical Center, 430 East 29th St, New York City, 10016 USA
| | - Eliane Candiani Arantes
- 1Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café s/n°, Monte Alegre, Ribeirão Preto, SP 14040-903 Brazil
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Liquid chromatography with alkylammonium formate ionic liquid mobile phases and fluorescence detection. J Chromatogr A 2018; 1559:128-135. [DOI: 10.1016/j.chroma.2018.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/05/2018] [Accepted: 03/12/2018] [Indexed: 02/05/2023]
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28
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Bowden NA, Sanders JP, Bruins ME. Solubility of the Proteinogenic α-Amino Acids in Water, Ethanol, and Ethanol-Water Mixtures. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2018; 63:488-497. [PMID: 29545650 PMCID: PMC5846082 DOI: 10.1021/acs.jced.7b00486] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/20/2017] [Indexed: 06/08/2023]
Abstract
The addition of organic solvents to α-amino acids in aqueous solution could be an effective method in crystallization. We reviewed the available data on the solubility of α-amino acids in water, water-ethanol mixtures, and ethanol at 298.15 K and 0.1 MPa. The solubility of l-alanine, l-proline, l-arginine, l-cysteine, and l-lysine in water and ethanol mixtures and the solubility of l-alanine, l-proline, l-arginine, l-cysteine, l-lysine, l-asparagine, l-glutamine, l-histidine, and l-leucine in pure ethanol systems were measured and are published here for the first time. The impact on the solubility of amino acids that can convert in solution, l-glutamic acid and l-cysteine, was studied. At lower concentrations, only the ninhydrin method and the ultraperfomance liquid chromatography (UPLC) method yield reliable results. In the case of α-amino acids that convert in solution, only the UPLC method was able to discern between the different α-amino acids and yields reliable results. Our results demonstrate that α-amino acids with similar physical structures have similar changes in solubility in mixed water/ethanol mixtures. The solubility of l-tryptophan increased at moderate ethanol concentrations.
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Affiliation(s)
- Nathan A. Bowden
- Biobased
Chemistry and Technology Group, ASFG, Wageningen
University and Research, Bornse Weilanden 9, Wageningen, 6708WG, The Netherlands
- School
of Life Sciences, Avans University of Applied
Science, Lovensdijkstraat
61-63, Breda, 4818AJ, The Netherlands
| | - Johan P.M. Sanders
- Biobased
Chemistry and Technology Group, ASFG, Wageningen
University and Research, Bornse Weilanden 9, Wageningen, 6708WG, The Netherlands
- Wageningen
Food & Biobased Research, Wageningen
University and Research, Bornse Weilanden 9, Wageningen, 6107WG, The Netherlands
| | - Marieke E. Bruins
- Wageningen
Food & Biobased Research, Wageningen
University and Research, Bornse Weilanden 9, Wageningen, 6107WG, The Netherlands
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Duque L, Körber M, Bodmeier R. Improving release completeness from PLGA-based implants for the acid-labile model protein ovalbumin. Int J Pharm 2018; 538:139-146. [DOI: 10.1016/j.ijpharm.2018.01.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/09/2018] [Accepted: 01/13/2018] [Indexed: 12/20/2022]
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Arbour CA, Stamatin RE, Stockdill JL. Sequence Diversification by Divergent C-Terminal Elongation of Peptides. J Org Chem 2018; 83:1797-1803. [PMID: 29293336 DOI: 10.1021/acs.joc.7b02655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Sequence diversification at the C terminus is traditionally limited by significant epimerization of the C-terminal residue during its activation toward nucleophilic attack, thus mandating repetition of the peptide synthesis for each targeted variation. Here, we accomplish divergent C-terminal elongation of a single peptide substrate with concomitant resin cleavage via displacement of an N-acyl urea moiety. Sterically hindered amino acids such as Ile and Pro are well-tolerated in this approach, which proceeds reasonable conversion and no detectable epimerization of the starting peptide's C-terminal amino acid.
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Affiliation(s)
- Christine A Arbour
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - Ramona E Stamatin
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - Jennifer L Stockdill
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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Mukherjee D, Ortiz Rodriguez LI, Hilaire MR, Troxler T, Gai F. 7-Cyanoindole fluorescence as a local hydration reporter: application to probe the microheterogeneity of nine water-organic binary mixtures. Phys Chem Chem Phys 2018; 20:2527-2535. [PMID: 29313858 DOI: 10.1039/c7cp07160d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Considerable efforts have been devoted to the development of spectroscopic probes that are sensitive to water and can be used to monitor, for example, biological and chemical processes involving dehydration or hydration. Continuing this line of research, herein we show that 7-cyanoindole can serve as a sensitive fluorescence probe of hydration as its fluorescence properties, including intensity, peak wavelength and lifetime, depend on the amount of water in nine water-organic solvent mixtures. Our results indicate that 7-cyanoindole is not only able to reveal the underlying microheterogeneity of these binary solvent systems, but also offers distinct advantages. These include: (1) its fluorescence intensity increases more than ten times upon going from a hydrated to a dehydrated environment; (2) its peak wavelength shifts as much as 35 nm upon dehydration; (3) its single-exponential fluorescence decay lifetime increases from 2.0 ns in water to 8-16 ns in water-organic binary mixtures, making it viable to distinguish between differently hydrated environments via fluorescence lifetime measurements; and (4) its absorption spectrum is significantly red-shifted from that of indole, making selective excitation of its fluorescence possible in the presence of naturally occurring amino-acid fluorophores. Moreover, we find that for seven binary mixtures the fluorescence lifetimes of 7-cyanoindole measured at solvent compositions where maximum microheterogeneity occurs correlate linearly with the peak wavenumbers of its fluorescence spectra obtained in the respective pure organic solvents. This suggests that the microheterogeneities of these binary mixtures bear certain similarity, a phenomenon that warrants further investigation.
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Affiliation(s)
- Debopreeti Mukherjee
- Department of Chemistry University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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Sirotkin VA, Kuchierskaya AA. α-chymotrypsin in water-acetone and water-dimethyl sulfoxide mixtures: Effect of preferential solvation and hydration. Proteins 2017; 85:1808-1819. [PMID: 28612358 DOI: 10.1002/prot.25334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/02/2017] [Accepted: 06/07/2017] [Indexed: 11/10/2022]
Abstract
We investigated water/organic solvent sorption and residual enzyme activity to simultaneously monitor preferential solvation/hydration of protein macromolecules in the entire range of water content at 25°C. We applied this approach to estimate protein destabilization/stabilization due to the preferential interactions of bovine pancreatic α-chymotrypsin with water-acetone (moderate-strength H-bond acceptor) and water-DMSO (strong H-bond acceptor) mixtures. There are three concentration regimes for the dried α-chymotrypsin. α-Chymotrypsin is preferentially hydrated at high water content. The residual enzyme activity values are close to 100%. At intermediate water content, the dehydrated α-chymotrypsin has a higher affinity for acetone/DMSO than for water. Residual enzyme activity is minimal in this concentration range. The acetone/DMSO molecules are preferentially excluded from the protein surface at the lowest water content, resulting in preferential hydration. The residual catalytic activity in the water-poor acetone is ∼80%, compared with that observed after incubation in pure water. This effect is very small for the water-poor DMSO. Two different schemes are operative for the hydrated enzyme. At high and intermediate water content, α-chymotrypsin exhibits preferential hydration. However, at intermediate water content, in contrast to the dried enzyme, the initially hydrated α-chymotrypsin possesses increased preferential hydration parameters. At low water content, no residual enzyme activity was observed. Preferential binding of DMSO/acetone to α-chymotrypsin was detected. Our data clearly demonstrate that the hydrogen bond accepting ability of organic solvents and the protein hydration level constitute key factors in determining the stability of protein-water-organic solvent systems.
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Affiliation(s)
- Vladimir A Sirotkin
- Department of Physical Chemistry, Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kazan, 420008, Russia
| | - Alexandra A Kuchierskaya
- Department of Physical Chemistry, Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kazan, 420008, Russia
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Punihaole D, Jakubek RS, Workman RJ, Marbella LE, Campbell P, Madura JD, Asher SA. Monomeric Polyglutamine Structures That Evolve into Fibrils. J Phys Chem B 2017; 121:5953-5967. [DOI: 10.1021/acs.jpcb.7b04060] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- David Punihaole
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ryan S. Jakubek
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Riley J. Workman
- Department
of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Lauren E. Marbella
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Patricia Campbell
- Department
of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, United States
| | - Jeffry D. Madura
- Department
of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Sanford A. Asher
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Sirotkin VA, Kuchierskaya AA. Lysozyme in water-acetonitrile mixtures: Preferential solvation at the inner edge of excess hydration. J Chem Phys 2017; 146:215101. [PMID: 28576085 DOI: 10.1063/1.4984116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Preferential solvation/hydration is an effective way for regulating the mechanism of the protein destabilization/stabilization. Organic solvent/water sorption and residual enzyme activity measurements were performed to monitor the preferential solvation/hydration of hen egg-white lysozyme at high and low water content in acetonitrile at 25 °C. The obtained results show that the protein destabilization/stabilization depends essentially on the initial hydration level of lysozyme and the water content in acetonitrile. There are three composition regimes for the dried lysozyme. At high water content, the lysozyme has a higher affinity for water than for acetonitrile. The residual enzyme activity values are close to 100%. At the intermediate water content, the dehydrated lysozyme has a higher affinity for acetonitrile than for water. A minimum on the residual enzyme activity curve was observed in this concentration range. At the lowest water content, the organic solvent molecules are preferentially excluded from the dried lysozyme, resulting in the preferential hydration. The residual catalytic activity is ∼80%, compared with that observed after incubation in pure water. Two distinct schemes are operative for the hydrated lysozyme. At high and intermediate water content, lysozyme is preferentially hydrated. However, in contrast to the dried protein, at the intermediate water content, the initially hydrated lysozyme has the increased preferential hydration parameters. At low water content, the preferential binding of the acetonitrile molecules to the initially hydrated lysozyme was detected. No residual enzyme activity was observed in the water-poor acetonitrile. Our data clearly show that the initial hydration level of the protein macromolecules is one of the key factors that govern the stability of the protein-water-organic solvent systems.
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Affiliation(s)
- Vladimir A Sirotkin
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Alexandra A Kuchierskaya
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
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Sirotkin VA, Kuchierskaya AA. Preferential Solvation/Hydration of α-Chymotrypsin in Water–Acetonitrile Mixtures. J Phys Chem B 2017; 121:4422-4430. [PMID: 28414445 DOI: 10.1021/acs.jpcb.7b01632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vladimir A. Sirotkin
- Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kremlevskaya str., 18, Kazan 420008, Russia
| | - Alexandra A. Kuchierskaya
- Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kremlevskaya str., 18, Kazan 420008, Russia
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Multiple, simultaneous, independent gradients for a versatile multidimensional liquid chromatography. Part II: Application 1 - Large increases in isoform resolution of human transferrin by use of dual simultaneous independent gradients of pH & acetonitrile on a mixed bed (anion exchange plus reversed phase) stationary phase. J Chromatogr A 2016; 1468:173-182. [DOI: 10.1016/j.chroma.2016.09.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 11/19/2022]
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Mohammad-Beigi H, Shojaosadati SA, Morshedi D, Mirzazadeh N, Arpanaei A. The Effects of Organic Solvents on the Physicochemical Properties of Human Serum Albumin Nanoparticles. IRANIAN JOURNAL OF BIOTECHNOLOGY 2016; 14:45-50. [PMID: 28959317 DOI: 10.15171/ijb.1168] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Recently, applications of albumin nanoparticles as drug delivery carriers have increased. Most toxicology studies have shown that surface chemistry and size of nanoparticles play an important role in biocompatibility and toxicity. OBJECTIVE The effect of desolvating agents with different chemical properties on the size of synthesized HSA NPs was investigated. MATERIALS AND METHODS Acetone, ethanol, methanol, and acetonitrile were used to synthesize HSA NPs with controllable size by desolvation method. Scanning electron microscopy (SEM), dynamic light scattering (DLS), and circular dichroism (CD) were employed to characterize produced particles. Finally, the toxicity of HSA NPs synthesized under different conditions was evaluated on PC-12 cells. RESULTS The sizes of synthesized particles differed according to the different solvents used. The sizes were 275.3 nm, 155.3 nm, 100.11 nm, and 66.2 nm for acetonitrile, ethanol, acetone, and methanol, respectively. CD showed that larger NPs had more changes in the secondary structures. Finally, the toxicity monitored on the cultured PC-12 cells showed no significant toxic effect through treating with these NPs at different concentrations (0-500 μg.mL-1). CONCLUSIONS The size of HSA NPs has a strong dependency on the desolvating agent. The mechanism in which the desolvating agent affects the size of HSA NPs is complex. Various factors such as dielectric constant, polarity, functional groups, and hydrogen bonding of the solvents have the potential to affect the size and structure of HSA NPs. CD analysis suggested that the solvent denaturing capability had a critical effect on the HSA particle size. The stronger denaturing capability of the solvent resulted in the larger HSA particle size.
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Affiliation(s)
- Hossein Mohammad-Beigi
- Biotechnology Group, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | | | - Dina Morshedi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Negar Mirzazadeh
- Biotechnology Group, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | - Ayyoob Arpanaei
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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Taghi Zafarani-Moattar M, Asadzadeh B. The solubility and stability of l-threonine in ionic liquids. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.11.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Pal S, Maity S, Sardar S, Chakraborty J, Halder UC. Insight into the co-solvent induced conformational changes and aggregation of bovine β-lactoglobulin. Int J Biol Macromol 2015; 84:121-34. [PMID: 26657584 DOI: 10.1016/j.ijbiomac.2015.11.055] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 09/05/2015] [Accepted: 11/20/2015] [Indexed: 11/15/2022]
Abstract
Many proteins form ordered irreversible aggregates called amyloid fibrils which are responsible for several neurodegenerative diseases. β-lactoglobulin (β-lg), an important globular milk protein, self-assembles to form amyloid-like fibrils on heating at low pH. The present study investigated the effects of two commonly used organic solvents acetonitrile (MeCN) and antimicrobial preservative benzyl alcohol (BA) on the conformation and self-assembly of β-lg at ambient condition. Both MeCN and BA induced a concentration-dependent conformational change showing exposure of hydrophobic patches, loss of tertiary structure and higher α-helical structure at moderate concentrations. In the presence of 50-80% (v/v) MeCN and 1.5-3% (v/v) BA further structural transitions from α-helical to non-native β-sheet structure were observed with a molten globule-like intermediate at 70% MeCN. These non-native β-sheet structures have high tendency to form aggregates. The formation of β-lg self-assembly was confirmed by Thioflavin T studies, Congo red assay, Rayleigh scattering and dynamic light scattering analysis. Transmission electron microscopy studies showed amyloid fibril formation in both MeCN and BA. Our results showed that BA enhances the unfolding and self-assembly of β-lg at much lower concentration than MeCN. Thus solvent composition forces the protein to achieve the non-native structures which are responsible for protein aggregation.
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Affiliation(s)
- Sampa Pal
- Organic Chemistry Section, Department of Chemistry, Jadavpur University, Kolkata, 700032, India
| | - Sanhita Maity
- Organic Chemistry Section, Department of Chemistry, Jadavpur University, Kolkata, 700032, India
| | - Subrata Sardar
- Organic Chemistry Section, Department of Chemistry, Jadavpur University, Kolkata, 700032, India
| | - Jishnu Chakraborty
- Organic Chemistry Section, Department of Chemistry, Jadavpur University, Kolkata, 700032, India
| | - Umesh Chandra Halder
- Organic Chemistry Section, Department of Chemistry, Jadavpur University, Kolkata, 700032, India.
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41
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Lambrecht MA, Rombouts I, Van Kelst L, Delcour JA. Impact of extraction and elution media on non-size effects in size exclusion chromatography of proteins. J Chromatogr A 2015; 1415:100-7. [DOI: 10.1016/j.chroma.2015.08.070] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/07/2015] [Accepted: 08/28/2015] [Indexed: 11/26/2022]
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42
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Tong X, Busk PK, Lange L, Pang J. New insights into the molecular mechanism of methanol-induced inactivation ofThermomyces lanuginosuslipase: a molecular dynamics simulation study. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1059938] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Non-fluorinated cosolvents: A potent amorphous aggregate inducer of metalloproteinase-conalbumin (ovotransferrin). Int J Biol Macromol 2015; 78:417-28. [DOI: 10.1016/j.ijbiomac.2015.04.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 10/23/2022]
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Kasai Y, Yoshida N, Nakano H. Theoretical analysis of co-solvent effect on the proton transfer reaction of glycine in a water-acetonitrile mixture. J Chem Phys 2015; 142:204103. [PMID: 26026430 DOI: 10.1063/1.4921432] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The co-solvent effect on the proton transfer reaction of glycine in a water-acetonitrile mixture was examined using the reference interaction-site model self-consistent field theory. The free energy profiles of the proton transfer reaction of glycine between the carboxyl oxygen and amino nitrogen were computed in a water-acetonitrile mixture solvent at various molar fractions. Two types of reactions, the intramolecular proton transfer and water-mediated proton transfer, were considered. In both types of the reactions, a similar tendency was observed. In the pure water solvent, the zwitterionic form, where the carboxyl oxygen is deprotonated while the amino nitrogen is protonated, is more stable than the neutral form. The reaction free energy is -10.6 kcal mol(-1). On the other hand, in the pure acetonitrile solvent, glycine takes only the neutral form. The reaction free energy from the neutral to zwitterionic form gradually increases with increasing acetonitrile concentration, and in an equally mixed solvent, the zwitterionic and neutral forms are almost isoenergetic, with a difference of only 0.3 kcal mol(-1). The free energy component analysis based on the thermodynamic cycle of the reaction also revealed that the free energy change of the neutral form is insensitive to the change of solvent environment but the zwitterionic form shows drastic changes. In particular, the excess chemical potential, one of the components of the solvation free energy, is dominant and contributes to the stabilization of the zwitterionic form.
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Affiliation(s)
- Yukako Kasai
- Department of Chemistry, Graduate School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Haruyuki Nakano
- Department of Chemistry, Graduate School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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Nahar LK, Andrews R, Paterson S. Validated Method for the Quantification of Buprenorphine in Postmortem Blood Using Solid-Phase Extraction and Two-Dimensional Gas Chromatography–Mass Spectrometry. J Anal Toxicol 2015; 39:519-25. [DOI: 10.1093/jat/bkv051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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46
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González JA, García de la Fuente I, Cobos JC, Alonso Tristán C, Sanz LF. Orientational Effects and Random Mixing in 1-Alkanol + Nitrile Mixtures. Ind Eng Chem Res 2015. [DOI: 10.1021/ie504282s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Juan Antonio González
- GETEF,
Departamento de Física Aplicada, Facultad de Ciencias, Universidad de Valladolid, Paseo de Belén, 7, 47011 Valladolid, Spain
| | - Isaías García de la Fuente
- GETEF,
Departamento de Física Aplicada, Facultad de Ciencias, Universidad de Valladolid, Paseo de Belén, 7, 47011 Valladolid, Spain
| | - José Carlos Cobos
- GETEF,
Departamento de Física Aplicada, Facultad de Ciencias, Universidad de Valladolid, Paseo de Belén, 7, 47011 Valladolid, Spain
| | - Cristina Alonso Tristán
- Departamento
Ingeniería Electromecánica, Escuela Politécnica
Superior, Universidad de Burgos, Avenida Cantabria s/n, 09006 Burgos, Spain
| | - Luis F. Sanz
- GETEF,
Departamento de Física Aplicada, Facultad de Ciencias, Universidad de Valladolid, Paseo de Belén, 7, 47011 Valladolid, Spain
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Nagana Gowda GA, Gowda YN, Raftery D. Expanding the limits of human blood metabolite quantitation using NMR spectroscopy. Anal Chem 2014; 87:706-15. [PMID: 25485990 PMCID: PMC4287831 DOI: 10.1021/ac503651e] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
A current challenge in metabolomics
is the reliable quantitation
of many metabolites. Limited resolution and sensitivity combined with
the challenges associated with unknown metabolite identification have
restricted both the number and the quantitative accuracy of blood
metabolites. Focused on alleviating this bottleneck in NMR-based metabolomics,
investigations of pooled human serum combining an array of 1D/2D NMR
experiments at 800 MHz, database searches, and spiking with authentic
compounds enabled the identification of 67 blood metabolites. Many
of these (∼1/3) are new compared with those reported previously
as a part of the Human Serum Metabolome Database. In addition, considering
both the high reproducibility and quantitative nature of NMR as well
as the sensitivity of NMR chemical shifts to altered sample conditions,
experimental protocols and comprehensive peak annotations are provided
here as a guide for identification and quantitation of the new pool
of blood metabolites for routine applications. Further, investigations
focused on the evaluation of quantitation using organic solvents revealed
a surprisingly poor performance for protein precipitation using acetonitrile.
One-third of the detected metabolites were attenuated by 10–67%
compared with methanol precipitation at the same solvent-to-serum
ratio of 2:1 (v/v). Nearly 2/3 of the metabolites were further attenuated
by up to 65% upon increasing the acetonitrile-to-serum ratio to 4:1
(v/v). These results, combined with the newly established identity
for many unknown metabolites in the NMR spectrum, offer new avenues
for human serum/plasma-based metabolomics. Further, the ability to
quantitatively evaluate nearly 70 blood metabolites that represent
numerous classes, including amino acids, organic acids, carbohydrates,
and heterocyclic compounds, using a simple and highly reproducible
analytical method such as NMR may potentially guide the evaluation
of samples for analysis using mass spectrometry.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, and ‡Department of Chemistry, University of Washington , Seattle, Washington 98109, United States
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49
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Kopanic JL, Al-mugotir MH, Kieken F, Zach S, Trease AJ, Sorgen PL. Characterization of the connexin45 carboxyl-terminal domain structure and interactions with molecular partners. Biophys J 2014; 106:2184-95. [PMID: 24853747 PMCID: PMC4052358 DOI: 10.1016/j.bpj.2014.03.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 03/19/2014] [Accepted: 03/31/2014] [Indexed: 02/02/2023] Open
Abstract
Mechanisms underlying the initiation and persistence of lethal cardiac rhythms are of significant clinical and scientific interests. Gap junctions are principally involved in forming the electrical connections between myocytes, and changes in distribution, density, and properties are consistent characteristics in arrhythmic heart disease. Therefore, understanding the structure and function of gap junctions during normal and abnormal impulse propagation are essential in the control of arrhythmias. For example, Cx45 is predominately expressed in the specialized myocytes of the impulse generation and conduction system. In both ventricular and atrial human working myocytes, Cx45 is present in very low quantities. However, a reduction in Cx43 coupled with an increased Cx45 protein levels within the ventricles have been observed after myocardial infarction and end-stage heart failure. Cx45 may influence electrical and/or metabolic coupling as a result of pathophysiological overexpression. Our goal was to identify mechanisms that could cause cellular coupling to be different between the cardiac connexins. Based upon the conserved transmembrane and extracellular loop segments, our focus was on identifying features within the divergent cytoplasmic portions. Here, we biophysically characterize the carboxyl-terminal domain of Cx45 (Cx45CT). Purification revealed the possibility of oligomeric species, which was confirmed by analytical ultracentrifugation experiments. Sedimentation equilibrium and circular dichroism studies of different Cx45CT constructs identified one region of α-helical structure (A333-N361) that mediates CT dimerization through hydrophobic contacts. Interestingly, the binding affinity of Cx45CT dimerization is 1000-fold stronger than Cx43CT dimerization. Cx45CT resonance assignments were also used to identify the binding sites and affinities of molecular partners involved in the Cx45 regulation; although none disrupted dimerization, many of these proteins interacted within one intrinsically disordered region (P278-P285). This domain has similarities with other cardiac connexins, and we propose they constitute a master regulatory domain, which contains overlapping molecular partner binding, cis-trans proline isomerization, and phosphorylation sites.
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Affiliation(s)
- Jennifer L Kopanic
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Mona H Al-mugotir
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Fabien Kieken
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sydney Zach
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Andrew J Trease
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Paul L Sorgen
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska.
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50
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Zhou L, Danielson ND. The ionic liquid isopropylammonium formate as a mobile phase modifier to improve protein stability during reversed phase liquid chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 940:112-20. [PMID: 24141045 PMCID: PMC4209125 DOI: 10.1016/j.jchromb.2013.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 10/26/2022]
Abstract
The room temperature ionic liquid isopropylammonium formate (IPAF) is studied as a reversed phase HPLC mobile phase modifier for separation of native proteins using a polymeric column and the protein stability is compared to that using acetonitrile (MeCN) as the standard organic mobile phase modifier. A variety of important proteins with different numbers of subunits are investigated, including non-subunit proteins: albumin, and amyloglucosidase (AMY); a two subunit protein: thyroglobulin (THY); and four subunit proteins: glutamate dehydrogenase (GDH) and lactate dehydrogenase (LDH). A significant enhancement in protein stability is observed in the chromatograms upon using IPAF as a mobile phase modifier. The first sharper peak at about 2min represented protein in primarily the native form and a second broader peak more retained at about 5-6min represented substantially denatured or possibly aggregated protein. The investigated proteins (except LDH) could maintain the native form within up to 50% IPAF, while a mobile phase, with as low as 10% MeCN, induced protein denaturation. The assay for pyruvate using LDH has further shown that enzymatic activity can be maintained up to 30% IPAF in water in contrast to no activity using 30% MeCN.
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Affiliation(s)
- Ling Zhou
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States.
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