1
|
Sawada K, Yamada T. Influence of the initial microbiota on eggplant shibazuke pickle and eggplant juice fermentation. Microbiol Spectr 2024; 12:e0046424. [PMID: 39016604 DOI: 10.1128/spectrum.00464-24] [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: 03/26/2024] [Accepted: 06/11/2024] [Indexed: 07/18/2024] Open
Abstract
The present study aimed to investigate the effects of the initial microbiota on microbial succession and metabolite transition during eggplant fermentation. Samples of traditional Japanese eggplant pickles, shibazuke, which were spontaneously fermented by plant-associated microbiota, were used for the analysis. Microbiota analysis indicated two successional patterns: early dominance of lactic acid bacteria superseded by aerobic bacteria and early dominance of lactic acid bacteria maintained to the end of the production process. Next, shibazuke production was modeled using filter-sterilized eggplant juice, fermenting the average composition of the initial shibazuke microbiota, which was artificially constructed from six major species identified during shibazuke production. In contrast to shibazuke production, all batches of eggplant juice fermentation showed almost identical microbial succession and complete dominance of Lactiplantibacillus plantarum in the final microbiota. These findings revealed the fate of initial microbiota under shibazuke production conditions: the early dominance of lactic acid bacteria that was maintained throughout, with L. plantarum ultimately predominating the microbiota. Furthermore, a comparison of the results between shibazuke production and eggplant juice fermentation suggested that L. plantarum is involved in the production of lactic acid, alanine, and glutamic acid during eggplant fermentation regardless of the final microbiota. IMPORTANCE The findings shown in this study provide insight into the microbial succession during spontaneous pickle fermentation and the role of Lactiplantibacillus plantarum in eggplant pickle production. Moreover, the novel method of using filter-sterilized vegetable juice with an artificial microbiota to emulate spontaneous fermentation can be applied to other spontaneously fermented products. This approach allows for the evaluation of the effect of specific initial microbiota in the absence of plant-associated bacteria from raw materials potentially promoting a greater understanding of microbial behavior in complex microbial ecosystems during vegetable fermentation.
Collapse
Affiliation(s)
- Kazunori Sawada
- Innovation Division, Gurunavi, Inc., Hibiya Mitsui Tower, Chiyoda-ku, Tokyo, Japan
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| |
Collapse
|
2
|
Hansen J, Sierra A, Mata S, Gassiot Ballbè E, Rey Lanaspa J, Welker F, Saña Seguí M, Clemente Conte I. Combining traceological analysis and ZooMS on Early Neolithic bone artefacts from the cave of Coro Trasito, NE Iberian Peninsula: Cervidae used equally to Caprinae. PLoS One 2024; 19:e0306448. [PMID: 38985699 PMCID: PMC11236160 DOI: 10.1371/journal.pone.0306448] [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: 04/15/2024] [Accepted: 06/18/2024] [Indexed: 07/12/2024] Open
Abstract
Few studies have combined the analysis of use-wear traces, traceology, and the proteomic taxonomic identification method Zooarchaeology by Mass Spectrometry (ZooMS). Traceology provides information on the usage, in this case, of bone artefacts, while ZooMS allows for taxonomic identifications where diagnostic features are otherwise gone. The approaches therefore offer complementary information on bone artefacts, allowing for insights into species selection strategies in bone tool manufacture and their subsequent use. Here we present a case study of 20 bone artefacts, mainly bone points, from the Early Neolithic cave site of Coro Trasito located on the southern slope of the Central Pyrenees. Hitherto, studies on Early Neolithic bone artefacts from the Iberian Peninsula have suggested based on morphological assessments that Ovis aries/Capra hircus constituted the majority of the bone material selected for bone tool production. However, the taxonomic identification in this study suggests that, at this site, Cervidae was selected equally to that of O. aries/C. hircus. Furthermore, bone artefacts made from Cervidae specimens seem to be utilised in a wider range of artefact types compared to O. aries/C. hircus. Coro Trasito's bone artefact species composition is probably site-specific to some degree, however, morphological assessments of bone artefacts might not be representative and could be biased towards certain species. Therefore, research on bone artefacts' usage could possibly gain new insights by implementing ZooMS in combination with traceology.
Collapse
Affiliation(s)
- Jakob Hansen
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Sierra
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Sergi Mata
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | | | - Javier Rey Lanaspa
- Departamento de Educación, Cultura y Deporte, Diputación General de Aragón, Zaragoza, Aragón, Spain
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Maria Saña Seguí
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Ignacio Clemente Conte
- Departamento de Arqueología y Antropología, Institución Milá y Fontanals de Estudios en Humanidades (IMF), del Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Barcelona, Spain
| |
Collapse
|
3
|
Morgan MB, Williams J, Breeze B, English N, Higdon N, Onthank K, Qualley DF. Synergistic and antagonistic interactions of oxybenzone and ocean acidification: new insight into vulnerable cellular processes in non-calcifying anthozoans. Front Physiol 2024; 14:1332446. [PMID: 38274044 PMCID: PMC10808722 DOI: 10.3389/fphys.2023.1332446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/28/2023] [Indexed: 01/27/2024] Open
Abstract
Cnidarians face significant threats from ocean acidification (OA) and anthropogenic pollutants such as oxybenzone (BP-3). The convergence of threats from multiple stressors is an important area to investigate because of potential significant synergistic or antagonistic interactions. Real-time quantitative PCR was performed to characterize the expression profiles of twenty-two genes of interest (GOI) in sea anemones (Exaiptasia diaphana) exposed to one of four treatments: 1) 96 h of OA conditions followed by a 4 h exposure to 20 ppb BP-3; 2) Exposure to 4 h 20 ppb BP-3 without 96 h of OA; 3) Exposure to 96 h of OA alone; or 4) laboratory conditions with no exposure to BP-3 and/or OA. These 22 GOIs represent cellular processes associated with proton-dependent transport, sodium-dependent transport, metal cation binding/transport, extracellular matrix, amino acid metabolism/transport, immunity, and/or steroidogenesis. These 22 GOIs provide new insight into vulnerable cellular processes in non-calcifying anthozoans exposed to OA and BP-3. Expression profiles were categorized as synergistic, antagonistic, or additive of BP-3 in the presence of OA. Two GOIs were synergistic. Fifteen GOIs were antagonistic and the remaining five GOIs were additive in response to BP-3 in acidified seawater. A subset of these GOIs appear to be candidate biomarkers for future in situ investigations. In human health, proton-dependent monocarboxylate transporters (MCTs) are promising pharmacological targets and recognized as potential biomarkers. By comparison, these same MCTs appear to be targets of xenobiotic chemical pollutants in cnidarian physiology. In the presence of BP-3, a network of collagen synthesis genes are upregulated and antagonistic in their expression profiles. Cytochrome b561 is a critical protein required for collagen synthesis and in silico modeling demonstrates BP-3 binds in the pocket of cytochrome b561. Understanding the underlying molecular mechanisms of "drug-like" compounds such as BP-3 may lead to a more comprehensive interpretation of transcriptional expression profiles. The collective antagonistic responses of GOIs associated with collagen synthesis strongly suggests these GOIs should be considered candidate biomarkers of effect. GOIs with synergistic and additive responses represent candidate biomarkers of exposure. Results show the effects of OA and BP-3 are interactive with respect to their impact on cnidarians. This investigation offers mechanistic data that supports the expression profiles and underpins higher order physiological responses.
Collapse
Affiliation(s)
- Michael B. Morgan
- Department of Biology, Berry College, Mount Berry, GA, United States
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, GA, United States
| | - Jacob Williams
- Department of Biology, Berry College, Mount Berry, GA, United States
| | - Barrett Breeze
- Department of Biology, Berry College, Mount Berry, GA, United States
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, GA, United States
| | - Nicholas English
- Department of Biology, Berry College, Mount Berry, GA, United States
| | - Nathaniel Higdon
- Department of Biology, Berry College, Mount Berry, GA, United States
| | - Kirt Onthank
- Department of Biology, Walla Walla University, College Place, WA, United States
| | - Dominic F. Qualley
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, GA, United States
| |
Collapse
|
4
|
Gouseti O, Larsen ME, Amin A, Bakalis S, Petersen IL, Lametsch R, Jensen PE. Applications of Enzyme Technology to Enhance Transition to Plant Proteins: A Review. Foods 2023; 12:2518. [PMID: 37444256 DOI: 10.3390/foods12132518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
As the plant-based food market grows, demand for plant protein is also increasing. Proteins are a major component in foods and are key to developing desired structures and textures. Seed storage proteins are the main plant proteins in the human diet. They are abundant in, for example, legumes or defatted oilseeds, which makes them an excellent candidate to use in the development of novel plant-based foods. However, they often have low and inflexible functionalities, as in nature they are designed to remain densely packed and inert within cell walls until they are needed during germination. Enzymes are often used by the food industry, for example, in the production of cheese or beer, to modify ingredient properties. Although they currently have limited applications in plant proteins, interest in the area is exponentially increasing. The present review first considers the current state and potential of enzyme utilization related to plant proteins, including uses in protein extraction and post-extraction modifications. Then, relevant opportunities and challenges are critically discussed. The main challenges relate to the knowledge gap, the high cost of enzymes, and the complexity of plant proteins as substrates. The overall aim of this review is to increase awareness, highlight challenges, and explore ways to address them.
Collapse
Affiliation(s)
- Ourania Gouseti
- Department of Food Science, University of Copenhagen, 1958 Copenhagen, Denmark
| | - Mads Emil Larsen
- Department of Food Science, University of Copenhagen, 1958 Copenhagen, Denmark
| | - Ashwitha Amin
- Department of Food Science, University of Copenhagen, 1958 Copenhagen, Denmark
| | - Serafim Bakalis
- Department of Food Science, University of Copenhagen, 1958 Copenhagen, Denmark
| | - Iben Lykke Petersen
- Department of Food Science, University of Copenhagen, 1958 Copenhagen, Denmark
| | - Rene Lametsch
- Department of Food Science, University of Copenhagen, 1958 Copenhagen, Denmark
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, 1958 Copenhagen, Denmark
| |
Collapse
|
5
|
Xia X, Zhou T, Zhang H, Cui H, Zhang F, Hayat K, Zhang X, Ho CT. Simultaneously Enhanced Formation of Pyrazines and Furans during Thermal Degradation of the Glycyl-l-glutamine Amadori Compound by Selected Exogenous Amino Acids and Appropriate Elevated Temperatures. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4346-4357. [PMID: 36880130 DOI: 10.1021/acs.jafc.3c00085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The Amadori compound of glucose and glycyl-l-glutamine (Gly-Gln-ARP) was prepared and characterized by UPLC-MS/MS and NMR. Gly-Gln-ARP could be thermally degraded into Gly-Gln and other secondary reaction products like glycyl-l-glutamic acid and its ARP via deamidation. The thermal processing temperature exerted a tremendous influence on the flavor formation of ARP. Furans were mainly formed at 100 °C, while an elevated temperature of 120 °C facilitated the massive accumulation of α-dicarbonyl compounds through the retro-aldolization of deoxyglucosone, and then increased the formation of pyrazines. The extra-added amino acids further promoted the formation of pyrazines at 120 °C, especially Glu, Lys, and His, further increasing the total concentration of pyrazines to 457 ± 6.26, 563 ± 65.5, and 411 ± 59.2 μg/L, respectively, exceeding the pure heated control at 140 °C (296 ± 6.67 μg/L). The total concentration of furans was enhanced to (20.7 × 103) ± 8.17 μg/L by extra-added Gln. Different increasing effects were observed on the type and flavor intensity of formed pyrazines and furans from different extra-added amino acids.
Collapse
Affiliation(s)
- Xue Xia
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu, P. R. China
| | - Tong Zhou
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu, P. R. China
| | - Han Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu, P. R. China
| | - Heping Cui
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu, P. R. China
| | - Foxin Zhang
- Anhui Province Key Laboratory of Functional Compound Seasoning, Anhui Qiang Wang Flavouring Food Co., Ltd., No. 1 Shengli Road, Jieshou, Fuyang 236500, Anhui, P. R. China
| | - Khizar Hayat
- Department of Kinesiology, Nutrition, and Health, Miami University, Oxford, Ohio 45056, United States
| | - Xiaoming Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu, P. R. China
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, 65 Dudley Road, New Brunswick, New Jersey 08901, United States
| |
Collapse
|
6
|
A Review on Forced Degradation Strategies to Establish the Stability of Therapeutic Peptide Formulations. Int J Pept Res Ther 2023. [DOI: 10.1007/s10989-023-10492-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
|
7
|
Lawson KE, Evans MN, Dekle JK, Adamczyk AJ. Computing the Differences between Asn-X and Gln-X Deamidation and Their Impact on Pharmaceutical and Physiological Proteins: A Theoretical Investigation Using Model Dipeptides. J Phys Chem A 2023; 127:57-70. [PMID: 36549007 DOI: 10.1021/acs.jpca.2c06511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein deamidation is a degradation mechanism that significantly impacts both pharmaceutical and physiological proteins. Deamidation impacts two amino acids, Asn and Gln, where the net neutral residues are converted into their acidic forms. While there are multiple similarities between the reaction mechanisms of the two residues, the impact of Gln deamidation has been noted to be most significant on physiological proteins while Asn deamidation has been linked to both pharmaceutical and physiological proteins. For this purpose, we sought to analyze the thermochemical and kinetic properties of the different reactions of Gln deamidation relative to Asn deamidation. In this study, we mapped the deamidation of Gln-X dipeptides into Glu-X dipeptides using density functional theory (DFT). Full network mapping facilitated the prediction of reaction selectivity between the two primary pathways, as well as between the two products of Gln-X deamidation as a function of solvent dielectric. To achieve this analysis, we studied a total of 77 dipeptide reactions per solvent dielectric (308 total reactions). Modeled at a neutral pH and using quantum chemical and statistical thermodynamic methods, we computed the following values: enthalpy of reaction (ΔHRXN), entropy (ΔSRXN), Gibbs free energy of reaction (ΔGRXN), activation energy (EA), and the Arrhenius preexponential factor (log(A)) for each dipeptide. Additionally, using chemical reaction principles, we generated a database of computed rate coefficients for all possible N-terminus Gln-X deamidation reactions at a neutral pH, predicted the most likely deamidation reaction mechanism for each dipeptide reaction, analyzed our results against our prior study on Asn-X deamidation, and matched our results against qualitative trends previously noted by experimental literature.
Collapse
Affiliation(s)
- Katherine E Lawson
- Department of Chemical Engineering, Auburn University, Auburn, Alabama36830, United States
| | - Megan N Evans
- Department of Chemical Engineering, Auburn University, Auburn, Alabama36830, United States
| | - Joseph K Dekle
- Department of Chemical Engineering, Auburn University, Auburn, Alabama36830, United States
| | - Andrew J Adamczyk
- Department of Chemical Engineering, Auburn University, Auburn, Alabama36830, United States
| |
Collapse
|
8
|
Liu H, Su Y, Fan Y, Zuo D, Xu J, Liu Y, Mei X, Huang H, Yang M, Zhu S. Exogenous leucine alleviates heat stress and improves saponin synthesis in Panax notoginseng by improving antioxidant capacity and maintaining metabolic homeostasis. FRONTIERS IN PLANT SCIENCE 2023; 14:1175878. [PMID: 37152124 PMCID: PMC10154563 DOI: 10.3389/fpls.2023.1175878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023]
Abstract
Panax notoginseng saponins (PNSs) are used as industrial raw materials to produce many drugs to treat cardio-cerebrovascular diseases. However, it is a heat-sensitive plant, and its large-scale artificial cultivation is impeded by high temperature stress, leading to decreases in productivity and PNSs yield. Here, we examined exogenous foliar leucine to alleviate heat stress and explored the underlying mechanism using metabolomics. The results indicated that 3 and 5 mM exogenous foliar leucine significantly alleviated heat stress in one-year- and two-year-old P. notoginseng in pots and field trials. Exogenous foliar leucine enhanced the antioxidant capacity by increasing the activities of antioxidant enzymes (POD, SOD) and the contents of antioxidant metabolites (amino acids). Moreover, exogenous foliar leucine enhanced carbohydrate metabolism, including sugars (sucrose, maltose) and TCA cycle metabolites (citric acid, aconitic acid, succinic acid and fumaric acid), in P. notoginseng leaves, stems, and fibrous roots to improve the energy supply of plants and further alleviate heat stress. Field experiments further verified that exogenous foliar leucine increased the productivity and PNSs accumulation in P. notoginseng. These results suggest that leucine application is beneficial for improving the growth and quality of P. notoginseng under heat stress. It is therefore possible to develop plant growth regulators based on leucine to improve the heat resistance of P. notoginseng and other crops.
Collapse
Affiliation(s)
- Haijiao Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yingwei Su
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yunxia Fan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Denghong Zuo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Jie Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yixiang Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Xinyue Mei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
- *Correspondence: Shusheng Zhu, ; Min Yang,
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
- *Correspondence: Shusheng Zhu, ; Min Yang,
| |
Collapse
|
9
|
Lebedev AT, Vasileva ID, Samgina TY. FT-MS in the de novo top-down sequencing of natural nontryptic peptides. MASS SPECTROMETRY REVIEWS 2022; 41:284-313. [PMID: 33347655 DOI: 10.1002/mas.21678] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
The present review covers available results on the application of FT-MS for the de novo sequencing of natural peptides of various animals: cones, bees, snakes, amphibians, scorpions, and so forth. As these peptides are usually bioactive, the animals efficiently use them as a weapon against microorganisms or higher animals including predators. These peptides represent definite interest as drugs of future generations since the mechanism of their activity is completely different in comparison with that of the modern antibiotics. Utilization of those peptides as antibiotics can eliminate the problem of the bacterial resistance development. Sequence elucidation of these bioactive peptides becomes even more challenging when the species genome is not available and little is known about the protein origin and other properties of those peptides in the study. De novo sequencing may be the only option to obtain sequence information. The benefits of FT-MS for the top-down peptide sequencing, the general approaches of the de novxxo sequencing, the difficult cases involving sequence coverage, isobaric and isomeric amino acids, cyclization of short peptides, the presence of posttranslational modifications will be discussed in the review.
Collapse
Affiliation(s)
- Albert T Lebedev
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Irina D Vasileva
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Y Samgina
- Organic Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
10
|
Fernando S. Pulse protein ingredient modification. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:892-897. [PMID: 34586636 DOI: 10.1002/jsfa.11548] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/09/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Increasing population and depletion of resources have paved the way to find sustainable and nutritious alternative protein sources. Pulses have been identified as a nutritious and inexpensive alternative source of protein that can meet this market demand. Pulses can be converted into protein concentrates and isolates through dry and wet separation techniques. Wet extraction results in relatively pure protein isolates but less sustainable due to higher energy requirements and high waste generation. Dry separation focuses on ingredient functionality rather than molecular level purity. These extracted pulse protein ingredients can be incorporated into different food systems to increase the nutritional value and to achieve the desired functionality. But many plant-based alternative proteins including pulses, face several formulation challenges especially in nutritional, sensory, and functional aspects. Native pulse protein ingredients can contain antinutrients, beany flavor, and undesirable functionality. Modification by biological (enzymatic, fermentation), chemical (acylation, deamidation, glycosylation, phosphorylation), and physical (cold plasma, extrusion, heat, high pressure, ultrasound) methods or a combination of these can improve pulse protein ingredients at the macro and micro level for their desired use. These modification processes will thermodynamically change the structural and conformational characteristics of proteins and expect to improve the quality. © 2021 Society of Chemical Industry.
Collapse
|
11
|
Mazzini G, Ricagno S, Caminito S, Rognoni P, Milani P, Nuvolone M, Basset M, Foli A, Russo R, Merlini G, Palladini G, Lavatelli F. Protease-sensitive regions in amyloid light chains: what a common pattern of fragmentation across organs suggests about aggregation. FEBS J 2021; 289:494-506. [PMID: 34482629 PMCID: PMC9292950 DOI: 10.1111/febs.16182] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/26/2021] [Accepted: 09/03/2021] [Indexed: 01/31/2023]
Abstract
Light‐chain (AL) amyloidosis is characterized by deposition of immunoglobulin light chains (LC) as fibrils in target organs. Alongside the full‐length protein, abundant LC fragments are always present in AL deposits. Herein, by combining gel‐based and mass spectrometry analyses, we identified and compared the fragmentation sites of amyloid LCs from multiple organs of an AL λ amyloidosis patient (AL‐55). The positions pinpointed here in kidney and subcutaneous fat, alongside those previously detected in heart of the same patient, were aligned and mapped on the LC’s dimeric and fibrillar states. All tissues contain fragmented LCs along with the full‐length protein; the fragment pattern is coincident across organs, although microheterogeneity exists. Multiple cleavage positions were detected; some are shared, whereas some are organ‐specific, likely due to a complex of proteases. Cleavage sites are concentrated in ‘proteolysis‐prone’ regions, common to all tissues. Several proteolytic sites are not accessible on native dimers, while they are compatible with fibrils. Overall, data suggest that the heterogeneous ensemble of LC fragments originates in tissues and is consistent with digestion of preformed fibrils, or with the hypothesis that initial proteolytic cleavage of the constant domain triggers the amyloidogenic potential of LCs, followed by subsequent proteolytic degradation. This work provides a unique set of molecular data on proteolysis from ex vivo amyloid, which allows discussing hypotheses on role and timing of proteolytic events occurring along amyloid formation and accumulation in AL patients.
Collapse
Affiliation(s)
- Giulia Mazzini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo and Università Degli Studi di Pavia, Italy
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Italy
| | - Serena Caminito
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo and Università Degli Studi di Pavia, Italy
| | - Paola Rognoni
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo and Università Degli Studi di Pavia, Italy
| | - Paolo Milani
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo and Università Degli Studi di Pavia, Italy
| | - Mario Nuvolone
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo and Università Degli Studi di Pavia, Italy
| | - Marco Basset
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo and Università Degli Studi di Pavia, Italy
| | - Andrea Foli
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo and Università Degli Studi di Pavia, Italy
| | - Rosaria Russo
- Dipartimento di Fisiopatologia Medico-Chirurgica e Dei Trapianti, Università Degli Studi di Milano, Italy
| | - Giampaolo Merlini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo and Università Degli Studi di Pavia, Italy
| | - Giovanni Palladini
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo and Università Degli Studi di Pavia, Italy
| | - Francesca Lavatelli
- Amyloidosis Treatment and Research Center, Fondazione IRCCS Policlinico San Matteo and Università Degli Studi di Pavia, Italy
| |
Collapse
|
12
|
Forensic proteomics. Forensic Sci Int Genet 2021; 54:102529. [PMID: 34139528 DOI: 10.1016/j.fsigen.2021.102529] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.
Collapse
|
13
|
Dang TT, Chan LY, Tombling BJ, Harvey PJ, Gilding EK, Craik DJ. In Planta Discovery and Chemical Synthesis of Bracelet Cystine Knot Peptides from Rinorea bengalensis. JOURNAL OF NATURAL PRODUCTS 2021; 84:395-407. [PMID: 33570395 DOI: 10.1021/acs.jnatprod.0c01065] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cyclotides are plant-derived peptides that have attracted interest as biocides and scaffolds for the development of stable peptide therapeutics. Cyclotides are characterized by their cyclic backbone and cystine knot framework, which engenders them with remarkably high stability. This study reports the cystine knot-related peptidome of Rinorea bengalensis, a small rainforest tree in the Violaceae family that is distributed from Australia westward to India. Surprisingly, many more acyclic knotted peptides (acyclotides) were discovered than cyclic counterparts (cyclotides), with 32 acyclotides and 1 cyclotide sequenced using combined transcriptome and proteomic analyses. Nine acyclotides were isolated and screened against a panel of mammalian cell lines, showing they had the cytotoxic properties normally associated with cyclotide-like peptides. NMR analysis of the acyclotide ribes 21 and 22 and the cyclotide ribe 33 confirmed that these peptides contained the cystine knot structural motif. The bracelet-subfamily cyclotide ribe 33 was amenable to chemical synthesis in reasonable yield, an achievement that has long eluded previous attempts to synthetically produce bracelet cyclotides. Accordingly, ribe 33 represents an exciting new bracelet cyclotide scaffold that can be subject to chemical modification for future molecular engineering applications.
Collapse
Affiliation(s)
- Tien T Dang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lai Y Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Benjamin J Tombling
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peta J Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
14
|
Fukuda TTH, Pereira CF, Melo WGP, Menegatti C, Andrade PHM, Groppo M, Lacava PT, Currie CR, Pupo MT. Insights Into the Ecological Role of Pseudomonas spp. in an Ant-plant Symbiosis. Front Microbiol 2021; 12:621274. [PMID: 33597940 PMCID: PMC7882492 DOI: 10.3389/fmicb.2021.621274] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Abstract
In the myrmecophytic mutualistic relationship between Azteca ants and Cecropia plants both species receive protection and exchange nutrients. The presence of microorganisms in this symbiotic system has been reported, and the symbiotic role of some fungi involved in the myrmecophytic interactions has been described. In this work we focus on bacteria within this mutualism, conducting isolations and screening for antimicrobial activities, genome sequencing, and biochemical characterization. We show that Pantoea, Rhizobium, Methylobacterium, Streptomyces and Pseudomonas are the most common cultivable genera of bacteria. Interestingly, Pseudomonas spp. isolates showed potent activity against 83% of the pathogens tested in our antimicrobial activity assays, including a phytopathogenic fungus isolated from Cecropia samples. Given the predicted nitrogen limitations associated with the fungal patches within this myrmecophyte, we performed nitrogen fixation analyses on the bacterial isolates within the Proteobacteria and show the potential for nitrogen fixation in Pseudomonas strains. The genome of one Pseudomonas strain was sequenced and analyzed. The gene cluster involved in the biosynthesis of cyclic lipodepsipeptides (CLPs) was identified, and we found mutations that may be related to the loss of function in the dual epimerization/condensation domains. The compound was isolated, and its structure was determined, corresponding to the antifungal viscosinamide. Our findings of diazotrophy and production of viscosinamide in multiple Pseudomonas isolates suggests that this bacterial genus may play an important role in the Cecropia-Azteca symbiosis.
Collapse
Affiliation(s)
- Taise T H Fukuda
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Camila F Pereira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Weilan G P Melo
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Carla Menegatti
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Paulo H M Andrade
- Laboratory of Microbiology and Biomolecules, Department of Morphology and Pathology, Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Milton Groppo
- Laboratory of Plant Systematics, Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Paulo T Lacava
- Laboratory of Microbiology and Biomolecules, Department of Morphology and Pathology, Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Mônica T Pupo
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| |
Collapse
|
15
|
Akharume FU, Aluko RE, Adedeji AA. Modification of plant proteins for improved functionality: A review. Compr Rev Food Sci Food Saf 2021; 20:198-224. [DOI: 10.1111/1541-4337.12688] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Felix U. Akharume
- Department of Biosystems and Agricultural Engineering University of Kentucky Lexington Kentucky USA
| | - Rotimi E. Aluko
- Department of Food and Human Nutritional Sciences and The Richardson Centre for Functional Foods and Nutraceuticals University of Manitoba Winnipeg Manitoba Canada
| | - Akinbode A. Adedeji
- Department of Biosystems and Agricultural Engineering University of Kentucky Lexington Kentucky USA
| |
Collapse
|
16
|
Drake JL, Whitelegge JP, Jacobs DK. First sequencing of ancient coral skeletal proteins. Sci Rep 2020; 10:19407. [PMID: 33173075 PMCID: PMC7655939 DOI: 10.1038/s41598-020-75846-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Here we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene fossil invertebrate, the stony coral Orbicella annularis. This fossil retains total hydrolysable amino acids of a roughly similar composition to extracts from modern O. annularis skeletons, with the amino acid data rich in Asx (Asp + Asn) and Glx (Glu + Gln) typical of invertebrate skeletal proteins. It also retains several proteins, including a highly acidic protein, also known from modern coral skeletal proteomes that we sequenced by LC-MS/MS over multiple trials in the best-preserved fossil coral specimen. A combination of degradation or amino acid racemization inhibition of trypsin digestion appears to limit greater recovery. Nevertheless, our workflow determines optimal samples for effective sequencing of fossil coral proteins, allowing comparison of modern and fossil invertebrate protein sequences, and will likely lead to further improvements of the methods. Sequencing of endogenous organic molecules in fossil invertebrate biominerals provides an ancient record of composition, potentially clarifying evolutionary changes and biotic responses to paleoenvironments.
Collapse
Affiliation(s)
- Jeana L Drake
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA.
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, USA.
- Department of Marine Biology, University of Haifa, Haifa, Israel.
| | | | - David K Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA.
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, USA.
| |
Collapse
|
17
|
Mass spectrometric analysis of protein deamidation – A focus on top-down and middle-down mass spectrometry. Methods 2020; 200:58-66. [DOI: 10.1016/j.ymeth.2020.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/16/2020] [Accepted: 08/06/2020] [Indexed: 11/22/2022] Open
|
18
|
Bristol AN, Carpenter BP, Davis AN, Kemp LK, Rangachari V, Karim S, Morgan SE. Aqueous RAFT Synthesis of Low Molecular Weight Anionic Polymers for Determination of Structure/Binding Interactions with Gliadin. Macromol Biosci 2020; 20:e2000125. [PMID: 32567240 DOI: 10.1002/mabi.202000125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/22/2020] [Indexed: 11/10/2022]
Abstract
Gliadin, a component of gluten and a known epitope, is implicated in celiac disease (CeD) and results in an inflammatory response in CeD patients when consumed. Acrylamide-based polyelectrolytes are employed as models to determine the effect of molecular weight and pendent group on non-covalent interaction modes with gliadin in vitro. Poly(sodium 2-acrylamido-2-methylpropane sulfonate) and poly(sodium 3-methylpropyl-3-butanoate) are synthesized via aqueous reversible addition fragmentation chain transfer (aRAFT) polymerization and characterized by gel permeation chromatography-multiangle laser light scattering. The polymer/gliadin blends are examined via circular dichroism, zeta potential measurements, 8-anilinonaphthalene-1-sulfonic acid fluorescence spectroscopy, and dynamic light scattering. Acrylamide polymers containing strong anionic pendent groups have a profound effect on gliadin secondary structure and solution behavior below the isoelectric point, while polymers containing hydrophobic character only have a minor impact. The polymers have little effect on gliadin secondary structure and solution behavior at the isoelectric point.
Collapse
Affiliation(s)
- Ashleigh N Bristol
- School of Polymer Science and Engineering, 118 College Dr., #5050, The University of Southern Mississippi, Hattiesburg, MS, 39406-5050, USA
| | - Brooke P Carpenter
- School of Polymer Science and Engineering, 118 College Dr., #5050, The University of Southern Mississippi, Hattiesburg, MS, 39406-5050, USA
| | - Ashley N Davis
- School of Polymer Science and Engineering, 118 College Dr., #5050, The University of Southern Mississippi, Hattiesburg, MS, 39406-5050, USA
| | - Lisa K Kemp
- School of Polymer Science and Engineering, 118 College Dr., #5050, The University of Southern Mississippi, Hattiesburg, MS, 39406-5050, USA
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, 39406-5050, USA
| | - Shahid Karim
- School of Biological, Environmental, and Earth Sciences, 118 College Dr., #5018, The University of Southern Mississippi, Hattiesburg, MS, 39406-5050, USA
| | - Sarah E Morgan
- School of Polymer Science and Engineering, 118 College Dr., #5050, The University of Southern Mississippi, Hattiesburg, MS, 39406-5050, USA
| |
Collapse
|
19
|
Ying Y, Li H. Recent progress in the analysis of protein deamidation using mass spectrometry. Methods 2020; 200:42-57. [PMID: 32544593 DOI: 10.1016/j.ymeth.2020.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/15/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
Deamidation is a nonenzymatic and spontaneous posttranslational modification (PTM) that introduces changes in both structure and charge of proteins, strongly associated with aging proteome instability and degenerative diseases. Deamidation is also a common PTM occurring in biopharmaceutical proteins, representing a major cause of degradation. Therefore, characterization of deamidation alongside its inter-related modifications, isomerization and racemization, is critically important to understand their roles in protein stability and diseases. Mass spectrometry (MS) has become an indispensable tool in site-specific identification of PTMs for proteomics and structural studies. In this review, we focus on the recent advances of MS analysis in protein deamidation. In particular, we provide an update on sample preparation, chromatographic separation, and MS technologies at multi-level scales, for accurate and reliable characterization of protein deamidation in both simple and complex biological samples, yielding important new insight on how deamidation together with isomerization and racemization occurs. These technological progresses will lead to a better understanding of how deamidation contributes to the pathology of aging and other degenerative diseases and the development of biopharmaceutical drugs.
Collapse
Affiliation(s)
- Yujia Ying
- School of Pharmaceutical Sciences, University of Sun Yat-sen University, No.132 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Huilin Li
- School of Pharmaceutical Sciences, University of Sun Yat-sen University, No.132 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.
| |
Collapse
|
20
|
Fujii N, Takata T, Kim I, Morishima K, Inoue R, Magami K, Matsubara T, Sugiyama M, Koide T. Asp isomerization increases aggregation of α-crystallin and decreases its chaperone activity in human lens of various ages. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140446. [PMID: 32442520 DOI: 10.1016/j.bbapap.2020.140446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
Abstract
α-Crystallin, comprising 40-50 subunits of αA- and αB-subunits, is a long-lived major soluble chaperone protein in lens. During aging, α-crystallin forms aggregates of high molecular weight (HMW) protein and eventually becomes water-insoluble (WI). Isomerization of Asp in α-crystallin has been proposed as a trigger of protein aggregation, ultimately leading to cataract formation. Here, we have investigated the relationship between protein aggregation and Asp isomerization of αA-crystallin by a series of analyses of the soluble α-crystallin, HMW and WI fractions from human lens samples of different ages (10-76 years). Analytical ultracentrifugation showed that the HMW fraction had a peak sedimentation coefficient of 40 S and a wide distribution of values (10-450 S) for lens of all ages, whereas the α-crystallin had a much smaller peak sedimentation coefficient (10-20 S) and was less heterogeneous, regardless of lens age. Measurement of the ratio of isomers (Lα-, Lβ-, Dα-, Dβ-) at Asp58, Asp91/92 and Asp151 in αA-crystallin by liquid chromatography-mass spectrometry showed that the proportion of isomers at all three sites increased in order of aggregation level (α-crystallin < HMW < WI fractions). Among the abnormal isomers of Asp58 and Asp151, Dβ-isomers were predominant with a very few exceptions. Notably, the chaperone activity of HMW protein was minimal for lens of all ages, whereas that of α-crystallin decreased with increasing lens age. Thus, abnormal aggregation caused by Asp isomerization might contribute to the loss of chaperone activity of α-crystallin in aged human lens.
Collapse
Affiliation(s)
- Noriko Fujii
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan.
| | - Takumi Takata
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Ingu Kim
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Kousuke Magami
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | | | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Tamaki Koide
- Rexxam Co., Ltd., Nishi-ku, Nagoya, Aichi 541-0054, Japan
| |
Collapse
|
21
|
Development of an efficient LC-MS peptide mapping method using accelerated sample preparation for monoclonal antibodies. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1137:121895. [DOI: 10.1016/j.jchromb.2019.121895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/24/2019] [Accepted: 11/18/2019] [Indexed: 11/30/2022]
|
22
|
Shao Q, Liu X, Su T, Ma C, Wang P. New Insights Into the Role of Seed Oil Body Proteins in Metabolism and Plant Development. FRONTIERS IN PLANT SCIENCE 2019; 10:1568. [PMID: 31921234 PMCID: PMC6914826 DOI: 10.3389/fpls.2019.01568] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/08/2019] [Indexed: 05/10/2023]
Abstract
Oil bodies (OBs) are ubiquitous dynamic organelles found in plant seeds. They have attracted increasing attention recently because of their important roles in plant physiology. First, the neutral lipids stored within these organelles serve as an initial, essential source of energy and carbon for seed germination and post-germinative growth of the seedlings. Secondly, they are involved in many other cellular processes such as stress responses, lipid metabolism, organ development, and hormone signaling. The biological functions of seed OBs are dependent on structural proteins, principally oleosins, caleosins, and steroleosins, which are embedded in the OB phospholipid monolayer. Oleosin and caleosin proteins are specific to plants and mainly act as OB structural proteins and are important for the biogenesis, stability, and dynamics of the organelle; whereas steroleosin proteins are also present in mammals and play an important role in steroid hormone metabolism and signaling. Significant progress using new genetic, biochemical, and imaging technologies has uncovered the roles of these proteins. Here, we review recent work on the structural or metabolic roles of these proteins in OB biogenesis, stabilization and degradation, lipid homeostasis and mobilization, hormone signal transduction, stress defenses, and various aspects of plant growth and development.
Collapse
Affiliation(s)
| | | | | | - Changle Ma
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Pingping Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| |
Collapse
|
23
|
Riggs DL, Silzel JW, Lyon YA, Kang AS, Julian RR. Analysis of Glutamine Deamidation: Products, Pathways, and Kinetics. Anal Chem 2019; 91:13032-13038. [PMID: 31498611 PMCID: PMC8805438 DOI: 10.1021/acs.analchem.9b03127] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Spontaneous chemical modifications play an important role in human disease and aging at the molecular level. Deamidation and isomerization are known to be among the most prevalent chemical modifications in long-lived human proteins and are implicated in a growing list of human pathologies, but the relatively minor chemical change associated with these processes has presented a long standing analytical challenge. Although the adoption of high-resolution mass spectrometry has greatly aided the identification of deamidation sites in proteomic studies, isomerization (and the isomeric products of deamidation) remain exceptionally challenging to characterize. Herein, we present a liquid chromatography/mass spectrometry-based approach for rapidly characterizing the isomeric products of Gln deamidation using diagnostic fragments that are abundantly produced and capable of unambiguously identifying both Glu and isoGlu. Importantly, the informative fragment ions are produced through orthogonal fragmentation pathways, thereby enabling the simultaneous detection of both isomeric forms while retaining compatibility with shotgun proteomics. Furthermore, the diagnostic fragments associated with isoGlu pinpoint the location of the modified residue. The utility of this technique is demonstrated by characterizing the isomeric products generated during in vitro aging of a series of glutamine-containing peptides. Sequence-dependent product profiles are obtained, and the abundance of deamidation-linked racemization is examined. Finally, comparisons are made between Gln deamidation, which is relatively poorly understood, and asparagine deamidation, which has been more thoroughly studied.
Collapse
Affiliation(s)
- Dylan L. Riggs
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Jacob W. Silzel
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yana A. Lyon
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Amrik S. Kang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
| |
Collapse
|
24
|
Apparent degradation forms of rhG-CSF under forced conditions: Insights for better quality-control of bioproducts. Anal Biochem 2019; 586:113440. [PMID: 31533024 DOI: 10.1016/j.ab.2019.113440] [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] [Received: 07/17/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 11/24/2022]
Abstract
Stability and quality control of therapeutic protein formulations is a substantial part of drug development process. The objective of this study is to obtain information about stability of a recombinant human granulocyte colony stimulating factor (rhG-CSF) against various stress factors. This will play a crucial role in the finished product formulation development. In this study, rhG-CSF was exposed to various chemical and physical stress conditions at different levels in order to identify degradation pathways and the nature of impurities generated. Experiments were performed by a combination of orthogonal analytical techniques (reversed phase chromatography (RP-HPLC), size exclusion chromatography (SEC-HPLC), polyacrylamide gel electrophoresis (SDS-PAGE) and isoelectric focusing (IEF)) to set and characterize the different degraded samples. The SEC-HPLC results suggest that the major degradation factors generating aggregated forms of the protein are basically thermal stress, freeze-thaw cycles and vortexing. Meanwhile, deamidated rhG-CSF was induced by basic pH as shown by IEF electrophoregram. As well, oxidized forms were generated increasingly with the time of exposure to hydrogen peroxide as outlined by RP-HPLC analysis. Based on these results, it was possible to define the storage and handling conditions of rhG-CSF finished product during its shelf life.
Collapse
|
25
|
Flores MA, Lazar IM. XMAn v2-a database of Homo sapiens mutated peptides. Bioinformatics 2019; 36:1311-1313. [PMID: 31539018 PMCID: PMC8215914 DOI: 10.1093/bioinformatics/btz693] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/12/2019] [Accepted: 09/03/2019] [Indexed: 01/31/2023] Open
Abstract
SUMMARY The 'Unknown Mutation Analysis (XMAn)' database is a compilation of Homo sapiens mutated peptides in FASTA format, that was constructed for facilitating the identification of protein sequence alterations by tandem mass spectrometry detection. The database comprises 2 539 031 non-redundant mutated entries from 17 599 proteins, of which 2 377 103 are missense and 161 928 are nonsense mutations. It can be used in conjunction with search engines that seek the identification of peptide amino acid sequences by matching experimental tandem mass spectrometry data to theoretical sequences from a database. AVAILABILITY AND IMPLEMENTATION XMAn v2 can be accessed from github.com/lazarlab/XMAnv2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
|
26
|
Qiu H, Wei R, Jaworski J, Boudanova E, Hughes H, VanPatten S, Lund A, Day J, Zhou Y, McSherry T, Pan CQ, Sendak R. Engineering an anti-CD52 antibody for enhanced deamidation stability. MAbs 2019; 11:1266-1275. [PMID: 31199181 PMCID: PMC6748592 DOI: 10.1080/19420862.2019.1631117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Deamidation evaluation and mitigation is an important aspect of therapeutic antibody developability assessment. We investigated the structure and function of the Asn-Gly deamidation in a human anti-CD52 IgG1 antibody light chain complementarity-determining region 1, and risk mitigation through protein engineering. Antigen binding affinity was found to decrease about 400-fold when Asn33 was replaced with an Asp residue to mimic the deamidation product, suggesting significant impacts on antibody function. Other variants made at Asn33 (N33H, N33Q, N33H, N33R) were also found to result in significant loss of antigen binding affinity. The co-crystal structure of the antigen-binding fragment bound to a CD52 peptide mimetic was solved at 2.2Å (PDB code 6OBD), which revealed that Asn33 directly interacts with the CD52 phosphate group via a hydrogen bond. Gly34, but sits away from the binding interface, rendering it more amendable to mutagenesis without affecting affinity. Saturation mutants at Gly34 were prepared and subjected to forced deamidation by incubation at elevated pH and temperature. Three mutants (G34R, G34K and G34Q) showed increased resistance to deamidation by LC-MS peptide mapping, while maintaining high binding affinity to CD52 antigen measured by Biacore. A complement -dependent cytotoxicity assay indicated that these mutants function by triggering antibody effector function. This study illustrates the importance of structure-based design and extensive mutagenesis to mitigate antibody developability issues.
Collapse
Affiliation(s)
- Huawei Qiu
- Biologics Research, Sanofi , Framingham , MA , USA
| | - Ronnie Wei
- Biologics Research, Sanofi , Framingham , MA , USA
| | | | | | | | | | - Anders Lund
- Biologics Development, Sanofi , Framingham , MA , USA
| | - Jaime Day
- Biologics Development, Sanofi , Framingham , MA , USA
| | - Yanfeng Zhou
- Biologics Research, Sanofi , Framingham , MA , USA
| | | | - Clark Q Pan
- Biologics Research, Sanofi , Framingham , MA , USA
| | | |
Collapse
|
27
|
Simpson JP, Fascione M, Bergström E, Wilson J, Collins MJ, Penkman KE, Thomas‐Oates J. Ionisation bias undermines the use of matrix-assisted laser desorption/ionisation for estimating peptide deamidation: Synthetic peptide studies demonstrate electrospray ionisation gives more reliable response ratios. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1049-1057. [PMID: 30908787 PMCID: PMC6594239 DOI: 10.1002/rcm.8441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 03/11/2019] [Accepted: 03/17/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Although mass spectrometry (MS) is routinely used to determine deamination in peptide mixtures, the effects of the choice of ionisation source have not yet been investigated. In particular, matrix-assisted laser desorption/ionisation (MALDI) has become a popular tool with which to measure levels of glutamine deamidation in ancient proteins. Here we use model synthetic peptides to rigorously compare MALDI and electrospray ionisation (ESI). METHODS We used two synthetic peptides, with glutamine (Q) in one substituted for glutamic acid (E) in the other, to investigate the suitability of MALDI and ESI sources for the assessment of deamidation in peptides using MS. We also compared measurements of the same Q- and E-containing peptide mixtures using two different mass analysers (time-of-flight (TOF) and Fourier transform ion cyclotron resonance (FT-ICR)). RESULTS When standard mixtures of the Q- and E-containing peptides were analysed using MALDI, under-representation of the E-containing peptide was observed. This observation was consistent between analyses carried out using either TOF or FT-ICR-MS. When the same mixtures were analysed using ESI FT-ICR-MS, no ionisation bias was observed. CONCLUSIONS MALDI may not be a suitable ionisation method for the determination of deamidation in peptide mixtures. However, ESI was successfully used to determine the ratio in known mixtures of Q- and E-containing peptides. These preliminary observations warrant further investigation into ionisation bias when measuring deamidation in other peptide sequences.
Collapse
Affiliation(s)
| | | | - Ed Bergström
- Department of ChemistryUniversity of YorkYorkUK
- Centre of Excellence in Mass SpectrometryUniversity of YorkYorkUK
| | - Julie Wilson
- Department of ChemistryUniversity of YorkYorkUK
- Department of MathematicsUniversity of YorkYorkUK
| | | | | | - Jane Thomas‐Oates
- Department of ChemistryUniversity of YorkYorkUK
- Centre of Excellence in Mass SpectrometryUniversity of YorkYorkUK
| |
Collapse
|
28
|
Kato K, Nakayoshi T, Kurimoto E, Oda A. Computational Studies on the Nonenzymatic Deamidation Mechanisms of Glutamine Residues. ACS OMEGA 2019; 4:3508-3513. [PMID: 31459565 PMCID: PMC6648516 DOI: 10.1021/acsomega.8b03199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/22/2019] [Indexed: 05/16/2023]
Abstract
The nonenzymatic deamidation reactions of asparagine (Asn) and glutamine (Gln) residues in proteins are associated with protein turnover and age-related diseases. The reactions are also believed to provide a molecular clock for biological processes. Although Gln deamidation is assumed to occur through the glutarimide intermediate, the mechanisms for this are unclear because under normal physiological conditions, Gln deamidation occurs relatively less frequently and at a lower rate than Asn deamidation. We investigate the mechanisms underlying glutarimide formation from Gln residues, which proceeds in two steps (cyclization and deammoniation) catalyzed by phosphate and carbonate. We also compare these reactions with noncatalytic mechanisms and water-catalyzed mechanisms. The calculations were performed on the model compound Ace-Gln-Nme (Ace = acetyl, Nme = methylamino) using the density functional theory with the B3LYP/6-31+G(d,p) level of theory. Our results suggest that all the catalysts used in our study can mediate the proton relays required for glutarimide formation. We further determined that the calculated activation barriers of the reactions catalyzed by phosphate ions (115 kJ mol-1) and carbonate ions (112 kJ mol-1) are sufficiently low for the reactions to occur under normal physiological conditions. We also show that nucleophilic enhancement of Nme nitrogen is essential for the cyclization of Gln residues.
Collapse
Affiliation(s)
- Koichi Kato
- College
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- E-mail: . Phone: +81-52-798-7474 (K.K.)
| | - Tomoki Nakayoshi
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Eiji Kurimoto
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Akifumi Oda
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
29
|
Łącki MK, Lermyte F, Miasojedow B, Startek MP, Sobott F, Valkenborg D, Gambin A. masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry. Anal Chem 2019; 91:1801-1807. [DOI: 10.1021/acs.analchem.8b01479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mateusz K. Łącki
- University Medical Center, Johannes Gutenberg University, Mainz D-55131, Germany
| | - Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp 2000, Belgium
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Błażej Miasojedow
- Department of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw 02-097, Poland
| | - Michał P. Startek
- Department of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw 02-097, Poland
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp 2000, Belgium
- Flemish Institute for Technological Research (VITO), Mol 2400, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt 3500, Belgium
| | - Anna Gambin
- Department of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw 02-097, Poland
| |
Collapse
|
30
|
Bahadoor A, Brauer EK, Bosnich W, Schneiderman D, Johnston A, Aubin Y, Blackwell B, Melanson JE, Harris LJ. Gramillin A and B: Cyclic Lipopeptides Identified as the Nonribosomal Biosynthetic Products of Fusarium graminearum. J Am Chem Soc 2018; 140:16783-16791. [PMID: 30395461 DOI: 10.1021/jacs.8b10017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The virulence and broad host range of Fusarium graminearum is associated with its ability to secrete an arsenal of phytotoxic secondary metabolites, including the regulated mycotoxins belonging to the deoxynivalenol family. The TRI genes responsible for the biosynthesis of deoxynivalenol and related compounds are usually expressed during fungal infection. However, the F. graminearum genome harbors an array of unexplored biosynthetic gene clusters that are also co-induced with the TRI genes, including the nonribosomal peptide synthetase 8 ( NRPS8) gene cluster. Here, we identify two bicyclic lipopeptides, gramillin A (1) and B (2), as the biosynthetic end products of NRPS8. Structural elucidation by high-resolution LC-MS and NMR, including 1H-15N-13C HNCO and HNCA on isotopically enriched compounds, revealed that the gramillins possess a fused bicyclic structure with ring closure of the main peptide macrocycle occurring via an anhydride bond. Through targeted gene disruption, we characterized the GRA1 biosynthetic gene and its transcription factor GRA2 in the NRPS8 gene cluster. Further, we show that the gramillins are produced in planta on maize silks, promoting fungal virulence on maize but have no discernible effect on wheat head infection. Leaf infiltration of the gramillins induces cell death in maize, but not in wheat. Our results show that F. graminearum deploys the gramillins as a virulence agent in maize, but not in wheat, thus displaying host-specific adaptation.
Collapse
Affiliation(s)
- Adilah Bahadoor
- Metrology , National Research Council Canada , Ottawa , Ontario K1A 0R6 , Canada
| | - Elizabeth K Brauer
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Whynn Bosnich
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Danielle Schneiderman
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Anne Johnston
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Yves Aubin
- Centre for Biologics Evaluation, Biologics, and Genetic Therapies Directorate , Health Canada , Ottawa , Ontario K1A 0K9 , Canada
| | - Barbara Blackwell
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| | - Jeremy E Melanson
- Metrology , National Research Council Canada , Ottawa , Ontario K1A 0R6 , Canada
| | - Linda J Harris
- Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , Ontario K1A 0C6 , Canada
| |
Collapse
|
31
|
Lermyte F, Valkenborg D, Loo JA, Sobott F. Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure. MASS SPECTROMETRY REVIEWS 2018; 37:750-771. [PMID: 29425406 PMCID: PMC6131092 DOI: 10.1002/mas.21560] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 05/11/2023]
Abstract
In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation. Although we focus on the two most widely used methods-ECD and ETD-we also discuss the use of other ion/electron, ion/ion, and ion/neutral fragmentation methods, useful for interrogation of a range of classes of biomolecules in positive- and negative-ion mode, and speculate about how this exciting field might evolve in the coming years.
Collapse
Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Agoralaan, Diepenbeek, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
32
|
Procopio N, Chamberlain AT, Buckley M. Exploring Biological and Geological Age-related Changes through Variations in Intra- and Intertooth Proteomes of Ancient Dentine. J Proteome Res 2018; 17:1000-1013. [PMID: 29356547 DOI: 10.1021/acs.jproteome.7b00648] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteomic analyses are becoming more widely used in archeology not only due to the greater preservation of proteins in ancient specimens than DNA but also because they can offer different information, particularly relating to compositional preservation and potentially a means to estimate biological and geological age. However, it remains unclear to what extent different burial environments impact these aspects of proteome decay. Teeth have to date been much less studied than bone but are ideal to explore how proteins decay with time due to the negligible turnover that occurs in dentine relative to bone. We investigated the proteome variability and deamidation levels of different sections of molar teeth from archeological bovine mandibles as well as their mandibular bone. We obtained a greater yield of proteins from the crown of the teeth but did not find differences between the different molars analyzed within each mandible. We also obtained the best variety of protein from a well-preserved mandible that was not the youngest one in terms of chronological age, showing the influence of the preservation conditions on the final proteomic outcome. Intriguingly, we also noticed an increase in abundance levels of fetuin-A in biologically younger mandibles as reported previously, but the opposite trend in tooth dentine. Interestingly, we observed higher glutamine deamidation levels in teeth from the geologically oldest mandible despite it being the biologically youngest specimen, showing that the archeological age strongly impacts on the level of deamidations observed, much more so than biological aging. This indicates that the glutamine deamidation ratio of selected peptides may act as a good predictor of the relative geochronological age of archeological specimens.
Collapse
Affiliation(s)
- Noemi Procopio
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Andrew T Chamberlain
- School of Earth and Environmental Sciences, The University of Manchester , Stopford Building, 99 Oxford Road, Manchester M13 9PG, United Kingdom
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
33
|
Hao P, Adav SS, Gallart-Palau X, Sze SK. Recent advances in mass spectrometric analysis of protein deamidation. MASS SPECTROMETRY REVIEWS 2017; 36:677-692. [PMID: 26763661 DOI: 10.1002/mas.21491] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 12/28/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
Protein deamidation has been proposed to represent a "molecular clock" that progressively disrupts protein structure and function in human degenerative diseases and natural aging. Importantly, this spontaneous process can also modify therapeutic proteins by altering their purity, stability, bioactivity, and antigenicity during drug synthesis and storage. Deamidation occurs non-enzymatically in vivo, but can also take place spontaneously in vitro, hence artificial deamidation during proteomic sample preparation can hamper efforts to identify and quantify endogenous deamidation of complex proteomes. To overcome this, mass spectrometry (MS) can be used to conduct rigorous site-specific characterization of protein deamidation due to the high sensitivity, speed, and specificity offered by this technique. This article reviews recent progress in MS analysis of protein deamidation and discusses the strengths and limitations of common "top-down" and "bottom-up" approaches. Recent advances in sample preparation methods, chromatographic separation, MS technology, and data processing have for the first time enabled the accurate and reliable characterization of protein modifications in complex biological samples, yielding important new data on how deamidation occurs across the entire proteome of human cells and tissues. These technological advances will lead to a better understanding of how deamidation contributes to the pathology of biological aging and major degenerative diseases. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:677-692, 2017.
Collapse
Affiliation(s)
- Piliang Hao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Sunil S Adav
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| |
Collapse
|
34
|
Sarg B, Faserl K, Lindner HH. Identification of Novel Site-Specific Alterations in the Modification Level of Myelin Basic Protein Isolated from Mouse Brain at Different Ages Using Capillary Electrophoresis-Mass Spectrometry. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/07/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Bettina Sarg
- Division of Clinical Biochemistry, Biocenter; Medical University of Innsbruck; Innsbruck Austria
| | - Klaus Faserl
- Division of Clinical Biochemistry, Biocenter; Medical University of Innsbruck; Innsbruck Austria
| | - Herbert H. Lindner
- Division of Clinical Biochemistry, Biocenter; Medical University of Innsbruck; Innsbruck Austria
| |
Collapse
|
35
|
Gallart-Palau X, Serra A, Sze SK. LERLIC-MS/MS for In-depth Characterization and Quantification of Glutamine and Asparagine Deamidation in Shotgun Proteomics. J Vis Exp 2017. [PMID: 28448026 DOI: 10.3791/55626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Characterization of protein deamidation is imperative to decipher the role(s) and potentialities of this protein posttranslational modification (PTM) in human pathology and other biochemical contexts. In order to perform characterization of protein deamidation, we have recently developed a novel long-length electrostatic repulsion-hydrophilic interaction chromatography-tandem mass spectrometry (LERLIC-MS/MS) method which can separate the glutamine (Gln) and asparagine (Asn) isoform products of deamidation from model compounds to highly complex biological samples. LERLIC-MS/MS is, therefore, the first shotgun proteomics strategy for the separation and quantification of Gln deamidation isoforms. We also demonstrate, as a novelty, that the sample processing protocol outlined here stabilizes the succinimide intermediate allowing its characterization by LERLIC-MS/MS. Application of LERLIC-MS/MS as shown in this video article can help to elucidate the currently unknown molecular arrays of protein deamidation. Additionally, LERLIC-MS/MS provides further understanding of the enzymatic reactions that encompass deamidation in distinct biological backgrounds.
Collapse
Affiliation(s)
- Xavier Gallart-Palau
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University
| | - Aida Serra
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University
| | - Siu Kwan Sze
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University;
| |
Collapse
|
36
|
Boles GC, Owen CJ, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of glutamic acid complexes with Zn2+and Cd2+. Phys Chem Chem Phys 2017; 19:12394-12406. [DOI: 10.1039/c7cp01786c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IRMPD of [Zn(Glu-H)ACN]+was particularly interesting because fragmentation of the amino acid was favored, rather than dissociation of the ACN ligand.
Collapse
Affiliation(s)
| | | | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- NL-6525 ED Nijmegen
- The Netherlands
| | | |
Collapse
|
37
|
Affiliation(s)
- Noemi Procopio
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
| | - Michael Buckley
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
| |
Collapse
|
38
|
Serra A, Gallart-Palau X, Wei J, Sze SK. Characterization of Glutamine Deamidation by Long-Length Electrostatic Repulsion-Hydrophilic Interaction Chromatography-Tandem Mass Spectrometry (LERLIC-MS/MS) in Shotgun Proteomics. Anal Chem 2016; 88:10573-10582. [DOI: 10.1021/acs.analchem.6b02688] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Aida Serra
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Juan Wei
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| |
Collapse
|
39
|
Black bean (Phaseolus vulgaris L.) protein hydrolysates: Physicochemical and functional properties. Food Chem 2016; 214:460-467. [PMID: 27507499 DOI: 10.1016/j.foodchem.2016.07.046] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 11/22/2022]
Abstract
Black bean protein hydrolysates obtained from pepsin and alcalase digestions until 120min of hydrolysis were evaluated by gel electrophoresis, relative fluorescence intensity, emulsifying properties, light micrograph of emulsions and in vitro antioxidant activity. The emulsion stability of the bean protein hydrolysates were evaluated during 30days of storage. The pepsin-treated bean protein hydrolysates presented higher degree of hydrolysis than the alcalase-treated protein hydrolysates. The alcalase-treated bean protein hydrolysates showed higher surface hydrophobicity. Moreover, the protein hydrolysates obtained with alcalase digestion presented higher emulsion stability during 30-days than those obtained from pepsin digestion. The protein concentrate and especially the hydrolysates obtained from alcalase digestion had good emulsion stability and antioxidant activity. Thus, they could be exploited as protein supplements in the diet as nutritional and bioactive foods.
Collapse
|
40
|
Kuznetsova KG, Trufanov PV, Moysa AA, Pyatnitskiy MA, Zgoda VG, Gorshkov MV, Moshkovskii SA. Threonine versus isothreonine in synthetic peptides analyzed by high-resolution liquid chromatography/tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1323-1331. [PMID: 27173114 DOI: 10.1002/rcm.7566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/15/2016] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE One of the problems in proteogenomic research aimed at identification of variant peptides is the presence of peptides with amino acid isomers of different origin in the analyzed samples. Among the most challenging examples are peptides with threonine and isothreonine (homoserine) in their sequences. Indeed, the latter residue may appear in vitro as a methionine substitution during sample preparation for shotgun proteome analysis. Yet, this substitution of Met to isoThr is not encoded genetically and should be unambiguously distinguished from, e.g., point mutations in proteins that result in Met conversion to Thr. METHODS In this work we compared tandem mass (MS/MS) spectra produced by an Orbitrap mass spectrometer of Thr- and isoThr-containing tryptic peptides and found a distinctive feature in their collisionally activated fragmentation patterns. RESULTS Up to 84% of MS/MS spectra for peptides containing isoThr residues have been positively specified. We also studied the differences in retention times for peptides containing Thr isoforms that can be further used for their distinction. CONCLUSIONS Threonine can be distinguished from isothreonine by its retention time and HCD fragmentation pattern, specifically relative intensity of the bn - product ion, which can be further used in proteomic research. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
| | - Pavel V Trufanov
- Institute of Biomedical Chemistry, Moscow, Russia
- Moscow State University, Biological Faculty, Moscow, Russia
| | - Alexander A Moysa
- Institute of Biomedical Chemistry, Moscow, Russia
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Mikhail V Gorshkov
- Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russia
| | - Sergei A Moshkovskii
- Institute of Biomedical Chemistry, Moscow, Russia
- Pirogov Russian National Medical University, Moscow, Russia
| |
Collapse
|
41
|
Schroeter ER, Cleland TP. Glutamine deamidation: an indicator of antiquity, or preservational quality? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:251-255. [PMID: 26689157 DOI: 10.1002/rcm.7445] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Much credence has been given in the paleoproteomic community to glutamine deamidation as a proxy for the age of proteins derived from fossil and subfossil material, and this modification has been invoked as a means for determining the endogeneity of molecules recovered from very old fossil specimens. METHODS We re-evaluated the relationship between glutamine deamidation and geologic time by examining previously published data from five recent mass spectrometry studies of archeaological fossils. Deamidation values recovered for fossils were graphed against their reported chronologic age using WebPlotDigitizer. RESULTS The experimental data that has been produced from fossil material to date show that the extent of glutamine deamidation does not correspond to the absolute age of the specimens being examined, but rather show extreme variation between specimens of similar age and taxonomic affinity. CONCLUSIONS Because deamidation rates and levels can be greatly affected by numerous chemical and environmental factors, we propose that glutamine deamidation is better suited as an indicator of preservational quality and/or environmental conditions than a mark of the endogeneity or authenticity of ancient proteins.
Collapse
Affiliation(s)
- Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12182, USA
| |
Collapse
|
42
|
Harwood MD, Achour B, Neuhoff S, Russell MR, Carlson G, Warhurst G. In Vitro-In Vivo Extrapolation Scaling Factors for Intestinal P-Glycoprotein and Breast Cancer Resistance Protein: Part I: A Cross-Laboratory Comparison of Transporter-Protein Abundances and Relative Expression Factors in Human Intestine and Caco-2 Cells. ACTA ACUST UNITED AC 2015; 44:297-307. [PMID: 26631742 DOI: 10.1124/dmd.115.067371] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/01/2015] [Indexed: 12/22/2022]
Abstract
Over the last 5 years the quantification of transporter-protein absolute abundances has dramatically increased in parallel to the expanded use of in vitro-in vivo extrapolation (IVIVE) and physiologically based pharmacokinetics (PBPK)-linked models, for decision-making in pharmaceutical company drug development pipelines and regulatory submissions. Although several research groups have developed laboratory-specific proteomic workflows, it is unclear if the large range of reported variability is founded on true interindividual variability or experimental variability resulting from sample preparation or the proteomic methodology used. To assess the potential for methodological bias on end-point abundance quantification, two independent laboratories, the University of Manchester (UoM) and Bertin Pharma (BPh), employing different proteomic workflows, quantified the absolute abundances of Na/K-ATPase, P-gp, and breast cancer resistance protein (BCRP) in the same set of biologic samples from human intestinal and Caco-2 cell membranes. Across all samples, P-gp abundances were significantly correlated (P = 0.04, Rs = 0.72) with a 2.4-fold higher abundance (P = 0.001) generated at UoM compared with BPh. There was a systematically higher BCRP abundance in Caco-2 cell samples quantified by BPh compared with UoM, but not in human intestinal samples. Consequently, a similar intestinal relative expression factor (REF), derived from distal jejunum and Caco-2 monolayer samples, between laboratories was found for P-gp. However, a 2-fold higher intestinal REF was generated by UoM (2.22) versus BPh (1.11). We demonstrate that differences in absolute protein abundance are evident between laboratories and they probably result from laboratory-specific methodologies relating to peptide choice.
Collapse
Affiliation(s)
- Matthew D Harwood
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Brahim Achour
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Sibylle Neuhoff
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Matthew R Russell
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Gordon Carlson
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Geoffrey Warhurst
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | | |
Collapse
|
43
|
Boles GC, Coates RA, Berden G, Oomens J, Armentrout PB. Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Glutamine Complexes with Zn2+ and Cd2+. J Phys Chem B 2015; 119:11607-17. [DOI: 10.1021/acs.jpcb.5b06528] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgia C. Boles
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Rebecca A. Coates
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
- Van‘t
Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| |
Collapse
|
44
|
Bodnar E, Ferreira Nascimento T, Girard L, Komatsu E, Lopez P, Gomes de Oliveira AG, Roy R, Smythe T, Zogbi Y, Spearman M, Tayi VS, Butler M, Perreault H. An integrated approach to analyze EG2-hFc monoclonal antibody N-glycosylation by MALDI-MS. CAN J CHEM 2015. [DOI: 10.1139/cjc-2015-0061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The characterization of the N-glycan portion of antibodies has been the subject of several studies involving mass spectrometry. In this article, a workflow is presented that starts with the expression of a monoclonal antibody (EG2-hFc) in Chinese hamster ovary cells and continues with Protein A purification of the antibody. Then the protocol continues with gel electrophoresis. Bands containing the heavy chain are cut and isolated from the gel followed by tryptic digestion to obtain peptides and glycopeptides. The enrichment of glycopeptides by C18 chromatography is described followed by characterization using positive and negative modes MALDI-MS and MS/MS. An exoglycosidase, beta-galactosidase, is used to verify anomericity of linkages in the glycan portion of glycopeptides. In the last step, glycans are detached from glycopeptides using PNGase F labelled with phehylhydrazine and characterized by MALDI-MS/MS. This workflow is reported for the first time for this particular antibody and presents a valuable approach for the analysis of N-glycans on most antibodies and glycoproteins.
Collapse
Affiliation(s)
- Edward Bodnar
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | | | - Lauren Girard
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Emy Komatsu
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Paul Lopez
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | | | - Rini Roy
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Tristan Smythe
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Yann Zogbi
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Maureen Spearman
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Venkata S. Tayi
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Michael Butler
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Hélène Perreault
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| |
Collapse
|
45
|
Maeda H, Takata T, Fujii N, Sakaue H, Nirasawa S, Takahashi S, Sasaki H, Fujii N. Rapid Survey of Four Asp Isomers in Disease-Related Proteins by LC-MS combined with Commercial Enzymes. Anal Chem 2014; 87:561-8. [DOI: 10.1021/ac504413e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Hiroki Maeda
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takumi Takata
- Research
Reactor Institute, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Norihiko Fujii
- Radioisotope
Research Center, Teikyo University, Kaga Itabashi-ku, Tokyo 173-8605, Japan
| | - Hiroaki Sakaue
- International University of Health and Welfare, Ohtawara, Tochigi 324-8501, Japan
| | - Satoru Nirasawa
- Japan International
Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
| | - Saori Takahashi
- Akita Research Institute
of Food and Brewing, Akita, 010-1623, Japan
| | - Hiroshi Sasaki
- Kanazawa Medical University, Kanazawa, Ishikawa 920-0293, Japan
| | - Noriko Fujii
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- Research
Reactor Institute, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| |
Collapse
|
46
|
Affiliation(s)
- Piliang Hao
- School of Biological Sciences, Nanyang Technological University Singapore
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University Singapore
| |
Collapse
|
47
|
Srzentić K, Fornelli L, Laskay ÜA, Monod M, Beck A, Ayoub D, Tsybin YO. Advantages of Extended Bottom-Up Proteomics Using Sap9 for Analysis of Monoclonal Antibodies. Anal Chem 2014; 86:9945-53. [DOI: 10.1021/ac502766n] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kristina Srzentić
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Luca Fornelli
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ünige A. Laskay
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michel Monod
- Department
of Dermatology, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Alain Beck
- Centre d’Immunologie Pierre Fabre, 74160 St. Julien-en-Genevois, France
| | - Daniel Ayoub
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Yury O. Tsybin
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
48
|
Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, University of Washington , Seattle, Washington 98195-1700, United States
| | | |
Collapse
|
49
|
Hurtado PP, O'Connor PB. Differentiation of isomeric amino acid residues in proteins and peptides using mass spectrometry. MASS SPECTROMETRY REVIEWS 2012; 31:609-25. [PMID: 22322410 DOI: 10.1002/mas.20357] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Characterization and differentiation of isomers in biological macromolecules using mass spectrometry is one of the most significant challenges facing scientists in the field. The capability of high-resolution MS instruments along with the development of new fragmentation methods now provides the ability to indirectly differentiate between some isomers. This ability has enabled mass spectrometry to evolve into a multidisciplinary technique incorporating areas such as pharmaceutical research, proteomics, polymer science, medicine, environmental chemistry, and recently archeology. This article aims to review recent developments in mass spectrometry methodologies in the identification of structural and spatial isomers in biological macromolecules, such as aspartic acid and isoaspartic acid (Asp/IsoAsp), leucine and isoleucine (Leu/Ile), glutamic acid and γ-glutamic acid, and D/L enantiomers.
Collapse
|
50
|
Wilson J, van Doorn NL, Collins MJ. Assessing the extent of bone degradation using glutamine deamidation in collagen. Anal Chem 2012; 84:9041-8. [PMID: 23030643 DOI: 10.1021/ac301333t] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Collagen peptides are analyzed using a low-cost, high-throughput method for assessing deamidation using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). For each chosen peptide, the theoretical distribution is calculated and the measured distribution for each sample compared with this to determine the extent of glutamine deamidation. The deamidation of glutamine (Q) to glutamic acid (E) results in a mass shift of +0.984 Da. Thus, from the resolution of our data, the second peak in the isotope distribution for a peptide containing one glutamine residue coincides with the first peak of the isotope distribution for the peptide in which the residue is deamidated. A genetic algorithm is used to determine the extent of deamidation that gives the best fit to the measured distribution. The method can be extended to peptides containing more than one glutamine residue. The extent of protein degradation assessed in this way could be used, for example, to assess the damage of collagen, and screen samples for radiocarbon dating and DNA analysis.
Collapse
Affiliation(s)
- Julie Wilson
- Department of Mathematics, University of York, York YO10 5YW, UK.
| | | | | |
Collapse
|