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Louati K, Maalej A, Kolsi F, Kallel R, Gdoura Y, Borni M, Hakim LS, Zribi R, Choura S, Sayadi S, Chamkha M, Mnif B, Khemakhem Z, Boudawara TS, Boudawara MZ, Safta F. Shotgun Proteomic-Based Approach with a Q-Exactive Hybrid Quadrupole-Orbitrap High-Resolution Mass Spectrometer for Protein Adductomics on a 3D Human Brain Tumor Neurospheroid Culture Model: The Identification of Adduct Formation in Calmodulin-Dependent Protein Kinase-2 and Annexin-A1 Induced by Pesticide Mixture. J Proteome Res 2023; 22:3811-3832. [PMID: 37906427 PMCID: PMC10696604 DOI: 10.1021/acs.jproteome.3c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/27/2023] [Accepted: 10/16/2023] [Indexed: 11/02/2023]
Abstract
Pesticides are increasingly used in combinations in crop protection, resulting in enhanced toxicities for various organisms. Although protein adductomics is challenging, it remains a powerful bioanalytical tool to check environmental exposure and characterize xenobiotic adducts as putative toxicity biomarkers with high accuracy, facilitated by recent advances in proteomic methodologies and a mass spectrometry high-throughput technique. The present study aims to predict the potential neurotoxicity effect of imidacloprid and λ-cyhalothrin insecticides on human neural cells. Our protocol consisted first of 3D in vitro developing neurospheroids derived from human brain tumors and then treatment by pesticide mixture. Furthermore, we adopted a bottom-up proteomic-based approach using nanoflow ultraperformance liquid chromatography coupled with a high-resolution mass spectrometer for protein-adduct analysis with prediction of altered sites. Two proteins were selected, namely, calcium-calmodulin-dependent protein kinase-II (CaMK2) and annexin-A1 (ANXA1), as key targets endowed with primordial roles. De novo sequencing revealed several adduct formations in the active site of 82-ANXA1 and 228-CaMK2 as a result of neurotoxicity, predicted by the added mass shifts for the structure of electrophilic precursors. To the best of our knowledge, our study is the first to adopt a proteomic-based approach to investigate in depth pesticide molecular interactions and their potential to adduct proteins which play a crucial role in the neurotoxicity mechanism.
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Affiliation(s)
- Kaouthar Louati
- Faculty
of Pharmacy, Laboratory of Pharmacology, Analytics & Galenic Drug
Development-LR12ES09, University of Monastir, Road Avicenne, Monastir 5000, Tunisia
| | - Amina Maalej
- Laboratory
of Environmental Bioprocesses, Centre of
Biotechnology of Sfax, Road of Sidi-Mansour, P.O. Box 1177, Sfax 3018, Tunisia
| | - Fatma Kolsi
- Department
of Neurosurgery, Habib Bourguiba University
Hospital, Road El Ain
km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Rim Kallel
- Laboratory
of Pathological Anatomy and Cytology, Habib
Bourguiba University Hospital, Road El Ain km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Yassine Gdoura
- Department
of Neurosurgery, Habib Bourguiba University
Hospital, Road El Ain
km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Mahdi Borni
- Department
of Neurosurgery, Habib Bourguiba University
Hospital, Road El Ain
km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Leila Sellami Hakim
- Laboratory
of Pathological Anatomy and Cytology, Habib
Bourguiba University Hospital, Road El Ain km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
| | - Rania Zribi
- Higher
Institute of Applied Studies to Humanities of Tunis (ISEAHT), University of Tunis, 11 Road of Jebel Lakdhar, Tunis 1005, Tunisia
| | - Sirine Choura
- Laboratory
of Environmental Bioprocesses, Centre of
Biotechnology of Sfax, Road of Sidi-Mansour, P.O. Box 1177, Sfax 3018, Tunisia
| | - Sami Sayadi
- Biotechnology
Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha 2713, Qatar
| | - Mohamed Chamkha
- Laboratory
of Environmental Bioprocesses, Centre of
Biotechnology of Sfax, Road of Sidi-Mansour, P.O. Box 1177, Sfax 3018, Tunisia
| | - Basma Mnif
- Department
of Bacteriology, Habib Bourguiba University
Hospital, Road El Ain
km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Zouheir Khemakhem
- Legal Medicine
Department, Habib Bourguiba University Hospital, Road El Ain km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Tahya Sellami Boudawara
- Laboratory
of Pathological Anatomy and Cytology, Habib
Bourguiba University Hospital, Road El Ain km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Mohamed Zaher Boudawara
- Department
of Neurosurgery, Habib Bourguiba University
Hospital, Road El Ain
km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Fathi Safta
- Faculty
of Pharmacy, Laboratory of Pharmacology, Analytics & Galenic Drug
Development-LR12ES09, University of Monastir, Road Avicenne, Monastir 5000, Tunisia
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Morais ATDB, Morais STB, Feitor JF, Santos WG, Gomes da Silva Catunda L, Walkling-Ribeiro M, Ahrne L, Cardoso DR. Impact of Physicochemical Modifications in Casein Promoted by UV-C on the Peptide Profile of Gastric Digestion and the Transepithelial Transport of Peptides. J Agric Food Chem 2023; 71:7495-7507. [PMID: 37157171 DOI: 10.1021/acs.jafc.3c00392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Caseins are the main proteins in milk, and their structure and spatial conformation are responsible for their slow digestion rate. The release of bioactive and β-casomorphin peptides from casein digestion may induce allergic responses during consumption. Spectroscopic techniques were used to observe the structural changes in casein conformation induced by Ultraviolet light irradiation (UV-C). Raman spectroscopy results showed more pronounced peaks at 618 and 640 cm-1 for phenylalanine and tyrosine moieties of the photolyzed micellar casein, respectively, suggesting changes in the micelle structure. The decrease in the intensity of Raman signals for tryptophan and tyrosine corroborates to the UV-C-induced modifications of the micelle structure. Particle size distribution showed a decrease in the average micelle size after 15 min of UV-C exposure, while low-temperature, long-time (LTLT) pasteurization led to the formation of large aggregates, as observed by atomic force microscopy. UV-C did not impact the formation or transport of peptides, as observed by using the Caco-2 cell as a model for peptide absorption. However, the absence of the opioid peptide SRYPSY from κ-casein and only 20% of the concentration of opioid peptide RYLGY were noted. This work demonstrated that UV-C can be utilized to induce the physicochemical modification of dairy products, promoting a higher digestion rate and reducing allergenicity.
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Affiliation(s)
- Aline Teixeira do Brasil Morais
- São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador São Carlense 400, CP 780, 13560-470 São Carlos, Brazil
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Sinara T B Morais
- São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador São Carlense 400, CP 780, 13560-470 São Carlos, Brazil
| | - Jessica F Feitor
- São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador São Carlense 400, CP 780, 13560-470 São Carlos, Brazil
| | - Willy Glen Santos
- São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador São Carlense 400, CP 780, 13560-470 São Carlos, Brazil
| | - Lucas Gomes da Silva Catunda
- São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador São Carlense 400, CP 780, 13560-470 São Carlos, Brazil
| | - Markus Walkling-Ribeiro
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Lilia Ahrne
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Daniel R Cardoso
- São Carlos Institute of Chemistry, University of São Paulo, Avenue Trabalhador São Carlense 400, CP 780, 13560-470 São Carlos, Brazil
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Songnaka N, Lertcanawanichakul M, Hutapea AM, Krobthong S, Yingchutrakul Y, Atipairin A. Purification and Characterization of Novel Anti-MRSA Peptides Produced by Brevibacillus sp. SPR-20. Molecules 2022; 27:molecules27238452. [PMID: 36500545 PMCID: PMC9738727 DOI: 10.3390/molecules27238452] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is listed as a high-priority pathogen because its infection is associated with a high mortality rate. It is urgent to search for new agents to treat such an infection. Our previous study isolated a soil bacterium (Brevibacillus sp. SPR-20), showing the highest antimicrobial activity against S. aureus TISTR 517 and MRSA strains. The present study aimed to purify and characterize anti-MRSA substances produced by SPR-20. The result showed that five active substances (P1-P5) were found, and they were identified by LC-MS/MS that provided the peptide sequences of 14-15 residues. Circular dichroism showed that all peptides contained β-strand and disordered conformations as the major secondary structures. Only P1-P4 adopted more α-helix conformations when incubated with 50 mM SDS. These anti-MRSA peptides could inhibit S. aureus and MRSA in concentrations of 2-32 μg/mL. P1 (NH2-VVVNVLVKVLPPPVV-COOH) had the highest activity and was identified as a novel antimicrobial peptide (AMP). The stability study revealed that P1 was stable in response to temperature, proteolytic enzymes, surfactant, and pH. The electron micrograph showed that P1 induced bacterial membrane damage when treated at 1× MIC in the first hour of incubation. The killing kinetics of P1 was dependent on concentration and time. Mechanisms of P1 on tested pathogens involved membrane permeability, leakage of genetic material, and cell lysis. The P1 peptide at a concentration up to 32 μg/mL showed hemolysis of less than 10%, supporting its safety for human erythrocytes. This study provides promising anti-MRSA peptides that might be developed for effective antibiotics in the post-antibiotic era.
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Affiliation(s)
- Nuttapon Songnaka
- School of Pharmacy, Walailak University, Nakhon Si Thammarat 80161, Thailand
| | | | - Albert M. Hutapea
- Faculty of Science, Universitas Advent Indonesia, Bandung 40559, Indonesia
| | - Sucheewin Krobthong
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yodying Yingchutrakul
- National Omics Center, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Apichart Atipairin
- School of Pharmacy, Walailak University, Nakhon Si Thammarat 80161, Thailand
- Drug and Cosmetics Excellence Center, Walailak University, Nakhon Si Thammarat 80161, Thailand
- Correspondence: ; Tel.: +66-7567-2832; Fax: +66-7567-2814
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Olagunju AI, Alashi AM, Omoba OS, Enujiugha VN, Aluko RE. Pigeon pea penta- and hexapeptides with antioxidant properties also inhibit renin and angiotensin-I-converting enzyme activities. J Food Biochem 2022; 46:e14485. [PMID: 36250929 DOI: 10.1111/jfbc.14485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 09/09/2022] [Accepted: 10/04/2022] [Indexed: 01/14/2023]
Abstract
Pigeon pea protein was sequentially digested with pepsin followed by pancreatin and the hydrolysate separated into 18 fractions using reversed-phase high-performance liquid chromatography. Fractions were analyzed for in vitro antioxidant properties (radical scavenging, metal chelation, and ferric iron reducing ability) in addition to inhibition of renin and angiotensin-converting enzyme (ACE). The most active fractions were analyzed by mass spectroscopy followed by identification of 10 peptide sequences (7 pentapeptides and 3 hexapeptides). All the peptides showed a wide range of multifunctional activity by scavenging hydroxyl (31.9-66.8%) and superoxide (25.6-100.0%) radicals in addition to ACE inhibition (7.4-100%) with significant (p < .05) differences between the peptides. AGVTVS, TKDIG, TSRLG, GRIST, and SGEKI were the most active; however, AGVTVS had the highest hydrophobic residue and exhibited the strongest activity against ACE, renin as well as superoxide and hydroxyl radicals. PRACTICAL APPLICATIONS: There is an increasing attraction of researchers to food peptides especially from legume proteins. Enzymatic digestion as well as high performance liquid chromatography (HPLC) purification has become an important process used to separate peptides with significant biological activities and health-promoting effects. There is useful information regarding the bioactive and functional (in vitro antioxidant, antidiabetic, in vitro/in vivo antihypertensive) properties of hydrolyzed and ultra-filtered pigeon pea fractions but scant research output still exists for purified peptides from pigeon pea establishing their therapeutic potential. The present study aimed to separate peptide fractions from pigeon pea hydrolysate and identify available amino acid sequences from the parent protein. Therefore, peptide sequences generated from the most bioactive fractions showed prospects for the expanded industrial utilization of pigeon pea. Further promoting its application as functional ingredient or additive for alleviating angiotensin-converting enzyme-related diseases.
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Affiliation(s)
- Aderonke I Olagunju
- Department of Food Science and Technology, Federal University of Technology, Akure, Nigeria
| | - Adeola M Alashi
- Research & Development, Custom Agricultural Intelligence Inc., Regina, Saskatchewan, Canada
| | - Olufunmilayo S Omoba
- Department of Food Science and Technology, Federal University of Technology, Akure, Nigeria
| | - Victor N Enujiugha
- Department of Food Science and Technology, Federal University of Technology, Akure, Nigeria
| | - Rotimi E Aluko
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Samgina TY, Vasileva ID, Trebse P, Torkar G, Surin AK, Meng Z, Zubarev RA, Lebedev AT. Mass Spectrometry Differentiation between Rana arvalis Populations Based on Their Skin Peptidome Composition. J Am Soc Mass Spectrom 2022; 33:1480-1491. [PMID: 35820801 DOI: 10.1021/jasms.2c00084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Skin secretion of amphibians often represents the only weapon of these species against pathogens and predators. Peptides constitute the major portion of active molecules of that weapon and may be treated as potential pharmaceuticals for future generations. The first step of their efficient use involves establishing of their primary structure, i.e., sequencing. De novo sequencing by means of mass spectrometry was applied to Rana arvalis species, collected in the spring 2021 in Central Slovenia (vicinity of Ljubljana). HPLC-ESI-HRMS/MS with Orbitrap instruments was used to establish the skin peptidome of these species and compare it with the earlier identified skin peptidome of the Moscow population of Rana arvalis. Application of CID, HCD, ETD, and EThcD enabled detecting and sequencing 18 peptides; five of them were novel and may be treated as possible biomarkers of the Ljubljana population of Rana arvalis. Interestingly, representatives of two peptide families (temporins and brevinins 2) were not found in the Moscow population. MS3 modes, first of all EThcD, demonstrated their great potential in the de novo sequencing, including extraction of the sequence information from the intact peptides with disulfide cycle (rana box) in their structure and differentiation of isomeric Leu/Ile residues. Thus, all six isomeric residues were reliably distinguished in the novel melittin-related peptide AK-23-1. In addition, another post-translational modification dealing with carbonylation of the N-terminal Gly of novel temporin AVa was established using the MS3 mode. The obtained results demonstrate the efficiency of the use of MS3 tools in proteomics/peptidomics.
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Affiliation(s)
- Tatiana Yu Samgina
- Lomonosov Moscow State University, Department of Organic Chemistry, Moscow 119991 Russia
| | - Irina D Vasileva
- Lomonosov Moscow State University, Department of Organic Chemistry, Moscow 119991 Russia
| | - Polonca Trebse
- University of Ljubljana Faculty of Health Sciences, Zdravstvena pot 5, Ljubljana 1000 Slovenia
- MASSECO d.o.o. Erazmova 20, Postojna 6230, Slovenia
| | - Gregor Torkar
- University of Ljubljana Faculty of Education, Department for Biology, Chemistry and Home Economics, Kardeljeva ploščad 16, Ljubljana 1000 Slovenia
| | - Alexey K Surin
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, Moscow 142290, Russia
| | - Zhaowei Meng
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, Stockholm 17177 Sweden
| | - Roman A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, Stockholm 17177 Sweden
| | - Albert T Lebedev
- Lomonosov Moscow State University, Department of Organic Chemistry, Moscow 119991 Russia
- MASSECO d.o.o. Erazmova 20, Postojna 6230, Slovenia
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Droctové L, Ciolek J, Mendre C, Chorfa A, Huerta P, Carvalho C, Gouin C, Lancien M, Stanajic-Petrovic G, Braco L, Blanchet G, Upert G, De Pauw E, Barbe P, Keck M, Mourier G, Mouillac B, Servent D, Rodríguez de la Vega RC, Quinton L, Gilles N. A new Kunitz-type snake toxin family associated with an original mode of interaction with the vasopressin 2 receptor. Br J Pharmacol 2022; 179:3470-3481. [PMID: 35122240 DOI: 10.1111/bph.15814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND AND PURPOSE Venomous animals express numerous Kunitz-type peptides. The mambaquaretin-1 (MQ1) identified from the Dendroaspis angusticeps venom is the most selective antagonist of the arginine-vasopressin V2 receptor (V2R) and the unique Kunitz-type peptide active on a GPCR. We aimed to exploit other mamba venoms to enlarge the V2R-Kunitz peptide family and gain insight into the MQ1 molecular mode of action. EXPERIMENTAL APPROACH We used a bio-guided screening assay to identify novel MQs and placed them phylogenetically. MQs were produced by solid phase peptide synthesis and characterized in vitro by binding and functional tests and in vivo by diuresis measurement in rats. KEY RESULTS Eight additional MQs were identified with nanomolar affinities for the V2R, all antagonists. MQs form a new subgroup in the Kunitz family, close to the V2R non-active dendrotoxins and to 2 V2R active cobra toxins. Sequence comparison between active and non-active V2R Kunitz peptides highlighted 5 positions, belong which, four are involved in V2R interaction and which belong to the 2 large MQ1 loops. We finally determined that 8 positions, part of these 2 loops, interact with the V2R. The variant MQ1-K39A showed higher affinity for the hV2R but not for the rat V2R. CONCLUSIONS AND IMPLICATIONS A new function and mode of action is now associated with the Kunitz-peptides. The number of MQ1 residues involved in V2R binding is large and may explain its absolute selectivity. MQ1-K39A represents the first step in the improvement of the MQ1 design for medicinal perspective.
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Affiliation(s)
- Laura Droctové
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Justyna Ciolek
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Christiane Mendre
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Amélia Chorfa
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Paola Huerta
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Chrystelle Carvalho
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Charlotte Gouin
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Manon Lancien
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Goran Stanajic-Petrovic
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Lorine Braco
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Guillaume Blanchet
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Gregory Upert
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Peggy Barbe
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Mathilde Keck
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Gilles Mourier
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Denis Servent
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
| | | | - Loïc Quinton
- Laboratory of Mass Spectrometry, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Nicolas Gilles
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Gif-sur-Yvette, France
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Malik WA, Javed S. Biochemical Characterization of Cellulase From Bacillus subtilis Strain and its Effect on Digestibility and Structural Modifications of Lignocellulose Rich Biomass. Front Bioeng Biotechnol 2022; 9:800265. [PMID: 34988069 PMCID: PMC8721162 DOI: 10.3389/fbioe.2021.800265] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial cellulases have become the mainstream biocatalysts due to their complex nature and widespread industrial applications. The present study reports the partial purification and characterization of cellulase from Bacillus subtilis CD001 and its application in biomass saccharification. Out of four different substrates, carboxymethyl cellulose, when amended as fermentation substrate, induced the highest cellulase production from B. subtilis CD001. The optimum activity of CMCase, FPase, and amylase was 2.4 U/ml, 1.5 U/ml, and 1.45 U/ml, respectively. The enzyme was partially purified by (NH4)2SO4 precipitation and sequenced through LC-MS/MS. The cellulase was found to be approximately 55 kDa by SDS-PAGE and capable of hydrolyzing cellulose, as confirmed by zymogram analysis. The enzyme was assigned an accession number AOR98335.1 and displayed 46% sequence homology with 14 peptide-spectrum matches having 12 unique peptide sequences. Characterization of the enzyme revealed it to be an acidothermophilic cellulase, having an optimum activity at pH 5 and a temperature of 60°C. Kinetic analysis of partially purified enzyme showed the Km and Vmax values of 0.996 mM and 1.647 U/ml, respectively. The enzyme activity was accelerated by ZnSO4, MnSO4, and MgSO4, whereas inhibited significantly by EDTA and moderately by β-mercaptoethanol and urea. Further, characterization of the enzyme saccharified sugarcane bagasse, wheat straw, and filter paper by SEM, ATR-FTIR, and XRD revealed efficient hydrolysis and structural modifications of cellulosic materials, indicating the potential industrial application of the B. subtilis CD001 cellulase. The findings demonstrated the potential suitability of cellulase from B. subtilis CD001 for use in current mainstream biomass conversion into fuels and other industrial processes.
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Affiliation(s)
- Waseem Ayoub Malik
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Saleem Javed
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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Larder CE, Iskandar MM, Kubow S. Gastrointestinal Digestion Model Assessment of Peptide Diversity and Microbial Fermentation Products of Collagen Hydrolysates. Nutrients 2021; 13:nu13082720. [PMID: 34444880 PMCID: PMC8401164 DOI: 10.3390/nu13082720] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 01/11/2023] Open
Abstract
Osteoarthritis (OA), the most common form of arthritis, is associated with metabolic diseases and gut microbiome dysbiosis. OA patients often take supplements of collagen hydrolysates (CHs) with a high peptide content. Following digestion, some peptides escape absorption to induce prebiotic effects via their colonic fermentation to generate short-chain fatty acids (SCFAs), branched-chain fatty acids (BCFAs) and colonic gases (NH4 and H2S). The capacity of CHs to generate microbial metabolites is unknown. Proteomic analysis of two CHs (CH-GL and CH-OPT) demonstrated different native peptide profiles with increased peptide diversity after in vitro gastric and small intestinal digestion. Subsequent 24 h fermentation of the CH digests in a dynamic gastrointestinal (GI) digestion model containing human fecal matter showed that CH-OPT increased (p < 0.05) H2S, SCFAs (propionic, butyric and valeric acids), BCFAs, and decreased NH4 in the ascending colon reactor with no major changes seen with CH-GL. No major effects were observed in the transverse and descending vessels for either CH. These findings signify that CHs can induce prebiotic effects in the ascending colon that are CH dependent. More studies are needed to determine the physiological significance of CH-derived colonic metabolites, in view of emerging evidence connecting the gut to OA and metabolic diseases.
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Class LC, Kuhnen G, Rohn S, Kuballa J. Diving Deep into the Data: A Review of Deep Learning Approaches and Potential Applications in Foodomics. Foods 2021; 10:1803. [PMID: 34441579 DOI: 10.3390/foods10081803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 01/18/2023] Open
Abstract
Deep learning is a trending field in bioinformatics; so far, mostly known for image processing and speech recognition, but it also shows promising possibilities for data processing in food analysis, especially, foodomics. Thus, more and more deep learning approaches are used. This review presents an introduction into deep learning in the context of metabolomics and proteomics, focusing on the prediction of shelf-life, food authenticity, and food quality. Apart from the direct food-related applications, this review summarizes deep learning for peptide sequencing and its context to food analysis. The review’s focus further lays on MS (mass spectrometry)-based approaches. As a result of the constant development and improvement of analytical devices, as well as more complex holistic research questions, especially with the diverse and complex matrix food, there is a need for more effective methods for data processing. Deep learning might offer meeting this need and gives prospect to deal with the vast amount and complexity of data.
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10
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Rajesh RP, Arun R, Selvam MM, Alphonse CRW, Rajasekar M, Franklin JB. Identification and characterisation of novel wasp mastoparans and chemotactic peptides from the venom of social wasp Polistes stigma (Hymenoptera: Vespidae: Polistinae). J Venom Res 2021; 11:16-20. [PMID: 34123360 PMCID: PMC8169029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022]
Abstract
Polistes stigma is a common social wasp found in continental Southeast Asia. Despite its wide distribution and abundance, hitherto, there are no studies on small or medium molecular weight components of the venom. For the first time, this study has described the amino acid sequences and its post-translation modifications (PTM's) of four wasp-mastoparans (Ps 1524, Ps 1540, Ps 1556 and Ps 1630), three chemotactic peptides (Ps1417, Ps1434 and Ps1474) and one more (Ps1549) lysine rich peptide from the venom of P. stigma. There were 27 mass traces obtained from the crude natural venom, in which the complete amino acid sequences of 8 peptides were solved. Further, single disulphide bonded peptides uncommon in wasp venoms were identified. The mastoparan peptides were rich in hydrophobic residues. In addition, the peptides Ps1549, Ps1630, Ps1434 and Ps1417 were found to have unusual PTM's of C-terminal amidation. This preliminary study comprehends the untapped compounds present in wasp venom that are equally valuable to widely studied venoms of snakes, spiders and cone snails.
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Affiliation(s)
- Rajaian Pushpabai Rajesh
- 1Molecular & Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119, India
| | - R. Arun
- 1Molecular & Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119, India
| | - M Masilamani Selvam
- 2Department of Biotechnology, Sathyabama Institute of Science and Technology, Chennai 600119, India
| | - Carlton Ranjith Wilson Alphonse
- 1Molecular & Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119, India
| | - M Rajasekar
- 1Molecular & Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai 600119, India
| | - Jayaseelan Benjamin Franklin
- 3Marine Conservation, Bombay Natural History Society, Hornbill House, SBS Road, Mumbai 400001, Maharashtra, India,*Correspondence to: Jayaseelan Benjamin Franklin, , Tel: +91 80729 68170
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Sonklin C, Alashi AM, Laohakunjit N, Aluko RE. Functional Characterization of Mung Bean Meal Protein-Derived Antioxidant Peptides. Molecules 2021; 26:1515. [PMID: 33802127 PMCID: PMC7999109 DOI: 10.3390/molecules26061515] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/02/2021] [Accepted: 03/08/2021] [Indexed: 11/30/2022] Open
Abstract
The aim of this work was to characterize the antioxidant properties of some of the peptides present in bromelain mung bean meal protein hydrolysate (MMPH). The MMPH was subjected to two rounds of bioassay-guided reversed-phase HPLC separation followed by peptide identification in the most potent fractions using tandem mass spectrometry. Twelve antioxidant peptides, namely, HC, CGN, LAN, CTN, LAF, CSGD, MMGW, QFAAD, ERF, EYW, FLQL, and QFAW were identified and assayed for antioxidant properties. CTN, HC, CGN, and CSGD were the most potent (p < 0.05) DPPH radical scavengers with EC50 values of 0.30, 0.29, 0.28, and 0.30 mg/mL, respectively, which are lower than the 0.03 mg/mL obtained for reduced glutathione (GSH). CTN, HC, CGN, and CSGD exhibited the most potent (p < 0.05) scavenging activities against hydroxyl and superoxide radicals with EC50 values that are similar to those of GSH. The cysteine-containing peptides also had stronger ferric reducing antioxidant power and metal chelation activity than peptides devoid of cysteine. In contrast, MMGW, ERF, and EYW had poor radical scavenging and metal chelation activities. We conclude that the availability of the sulfhydryl group may have enhanced antioxidant potency while the presence of bulky groups such phenylalanine and tryptophan had an opposite effect.
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Affiliation(s)
- Chanikan Sonklin
- Department of Industrial Chemistry, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, 1518 Pracharat 1 Rd., Wongsawang, Bangsue, Bangkok 10800, Thailand;
| | - Adeola M. Alashi
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
| | - Natta Laohakunjit
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, 49 Tein-talay 25 Rd., Tha-kam, Bangkhuntein, Bangkok 10150, Thailand;
| | - Rotimi E. Aluko
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
- Richardson Centre for Functional Foods and Nutraceuticals, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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12
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Yang C, Liu J, Hu Y, Dai Z, Liang Z, Shan Y, Zhang L, Zhang Y. Combination of continuous digestion by peptidase and spectral similarity comparisons for peptide sequencing. J Sep Sci 2021; 43:3665-3673. [PMID: 33405339 DOI: 10.1002/jssc.202000459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 11/10/2022]
Abstract
Peptide sequencing is critical to the quality control of peptide drugs and functional studies of active peptides. A combination of peptidase digestion and mass spectrometry technology is common for peptide sequencing. However, such methods often cannot obtain the complete sequence of a peptide due to insufficient amino acid sequence information. Here, we developed a method of generating full peptide ladders and comparing their MS2 spectral similarities. The peptide ladders, of which each component was different from the next component with one residue, were generated by continuous digestion by peptidase (carboxypeptidase Y and aminopeptidase). Then, based on the characteristics of peptide ladders, complete sequencing was realized by comparing MS2 spectral similarity of the generated peptide ladders. The complete amino acid sequences of bivalirudin, adrenocorticotropic hormone, and oxytocin were determined with high accuracy. This approach is beneficial to the quality control of drug peptides as well as the identification of novel bioactive peptides.
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Affiliation(s)
- Chao Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Jianhui Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Yechen Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Zhongpeng Dai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Yichu Shan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
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13
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Baba WN, Mudgil P, Kamal H, Kilari BP, Gan CY, Maqsood S. Identification and characterization of novel α-amylase and α-glucosidase inhibitory peptides from camel whey proteins. J Dairy Sci 2020; 104:1364-1377. [PMID: 33309363 DOI: 10.3168/jds.2020-19271] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/13/2020] [Indexed: 01/01/2023]
Abstract
This study explores the inhibitory properties of camel whey protein hydrolysates (CWPH) toward α-amylase (AAM) and α-glucosidase (AG). A general full factorial design (3 × 3) was applied to study the effect of temperature (30, 37, and 45°C), time (120, 240, and 360 min), and enzyme (pepsin) concentration (E%; 0.5, 1, and 2%). The results showed that maximum degree of hydrolysis was obtained when hydrolysis was carried out at higher temperature (45°C; P < 0.05), compared with lower temperatures of 30 and 37°C. Electrophoretic pattern displays degradation of all protein bands upon hydrolysis by pepsin at various hydrolysis conditions applied. All the 27 CWPH generated showed significant AAM and AG inhibitory potential as indicated by their lower IC50 values (mg/mL) compared with intact whey proteins. In total 196 peptides were identified from selected hydrolysates and 15 potential peptides (PepSite score > 0.8; http://pepsite2.russelllab.org/) were explored via in silico approach. Novel peptides PAGNFLMNGLMHR, PAVACCLPPLPCHM, MLPLMLPFTMGY, and PAGNFLPPVAAAPVM were identified as potential inhibitors for both AAM and AG due to their high number of binding sites and highest binding probability toward the target enzymes. CCGM and MFE, as well as FCCLGPVPP were identified as AG and AAM inhibitory peptides, respectively. This is the first study that reports novel AG and AAM inhibitory peptides from camel whey proteins. The future direction for this research involves synthesis of these potential AG and AAM inhibitory peptides in a pure form and investigate their antidiabetic properties in the in vitro, as well as in vivo models. Thus, CWPH can be considered for potential applications in glycaemic regulation.
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Affiliation(s)
- Waqas N Baba
- Department of Food, Nutrition and Health, College of Food and Agriculture, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
| | - Priti Mudgil
- Department of Food, Nutrition and Health, College of Food and Agriculture, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
| | - Hina Kamal
- Department of Food, Nutrition and Health, College of Food and Agriculture, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
| | - Bhanu Priya Kilari
- Department of Food, Nutrition and Health, College of Food and Agriculture, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
| | - Chee-Yuen Gan
- Analytical Biochemistry Research Centre (ABrC), Universiti Sains Malaysia, 11800 USM, Penang, Malaysia.
| | - Sajid Maqsood
- Department of Food, Nutrition and Health, College of Food and Agriculture, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates.
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Abd El-Aziz TM, Jaquillard L, Bourgoin-Voillard S, Martinez G, Triquigneaux M, Zoukimian C, Combemale S, Hograindleur JP, Al Khoury S, Escoffier J, Michelland S, Bulet P, Beroud R, Seve M, Arnoult C, De Waard M. Identification, Characterization and Synthesis of Walterospermin, a Sperm Motility Activator from the Egyptian Black Snake Walterinnesia aegyptia Venom. Int J Mol Sci 2020; 21:E7786. [PMID: 33096770 DOI: 10.3390/ijms21207786] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 01/02/2023] Open
Abstract
Animal venoms are small natural mixtures highly enriched in bioactive components. They are known to target at least two important pharmacological classes of cell surface receptors: ion channels and G protein coupled receptors. Since sperm cells express a wide variety of ion channels and membrane receptors, required for the control of cell motility and acrosome reaction, two functions that are defective in infertility issues, animal venoms should contain interesting compounds capable of modulating these two essential physiological functions. Herein, we screened for bioactive compounds from the venom of the Egyptian black snake Walterinnesia aegyptia (Wa) that possess the property to activate sperm motility in vitro from male mice OF1. Using RP-HPLC and cation exchange chromatography, we identified a new toxin of 6389.89 Da (termed walterospermin) that activates sperm motility. Walterospermin was de novo sequenced using a combination of matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF/TOF MS/MS) and liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF MS/MS) following reduction, alkylation, and enzymatic proteolytic digestion with trypsin, chymotrypsin or V8 protease. The peptide is 57 amino acid residues long and contains three disulfide bridges and was found to be identical to the previously cloned Wa Kunitz-type protease inhibitor II (Wa Kln-II) sequence. Moreover, it has strong homology with several other hitherto cloned Elapidae and Viperidae snake toxins suggesting that it belongs to a family of compounds able to regulate sperm function. The synthetic peptide shows promising activation of sperm motility from a variety of species, including humans. Its fluorescently-labelled analog predominantly marks the flagellum, a localization in agreement with a receptor that controls motility function.
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Kusumah J, Real Hernandez LM, Gonzalez de Mejia E. Antioxidant Potential of Mung Bean ( Vigna radiata) Albumin Peptides Produced by Enzymatic Hydrolysis Analyzed by Biochemical and In Silico Methods. Foods 2020; 9:E1241. [PMID: 32899856 DOI: 10.3390/foods9091241] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022] Open
Abstract
The objective of this study was to investigate the biochemical antioxidant potential of peptides derived from enzymatically hydrolyzed mung bean (Vigna radiata) albumins using an 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging assay, a ferrous ion chelating assay and an oxygen radical absorbance capacity (ORAC) assay. Peeled raw mung bean was ground into flour and mixed with buffer (pH 8.3, 1:20 w/v ratio) before being stirred, then filtered using 3 kDa and 30 kDa molecular weight cut-off (MWCO) centrifugal filters to obtain albumin fraction. The albumin fraction then underwent enzymatic hydrolysis using either gastrointestinal enzymes (pepsin and pancreatin) or thermolysin. Peptides in the hydrolysates were sequenced. The peptides showed low ABTS radical-scavenging activity (90-100 μg ascorbic acid equivalent/mL) but high ferrous ion chelating activity (1400-1500 μg EDTA equivalent/mL) and ORAC values (>120 μM Trolox equivalent). The ferrous ion chelating activity was enzyme- and hydrolysis time-dependent. For thermolysin hydrolysis, there was a drastic increase in ferrous ion chelating activity from t = 0 (886.9 μg EDTA equivalent/mL) to t = 5 min (1559.1 μg EDTA equivalent/mL) before plateauing. For pepsin-pancreatin hydrolysis, there was a drastic decrease from t = 0 (878.3 μg EDTA equivalent/mL) to t = 15 (138.0 μg EDTA equivalent/mL) after pepsin was added, but this increased from t = 0 (131.1 μg EDTA equivalent/mL) to t = 15 (1439.2 μg EDTA equivalent/mL) after pancreatin was added. There was no significant change in ABTS radical scavenging activity or ORAC values throughout different hydrolysis times for either the thermolysin or pepsin-pancreatin hydrolysis. Overall, mung bean hydrolysates produced peptides with high potential antioxidant capacity, being particularly effective ferrous ion chelators. Other antioxidant assays that use cellular lines should be performed to measure antioxidant capacity before animal and human studies.
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16
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Behsaz B, Mohimani H, Gurevich A, Prjibelski A, Fisher M, Vargas F, Smarr L, Dorrestein PC, Mylne JS, Pevzner PA. De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Cell Syst 2020; 10:99-108.e5. [PMID: 31864964 DOI: 10.1016/j.cels.2019.11.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/18/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022]
Abstract
Cyclic and branch cyclic peptides (cyclopeptides) represent a class of bioactive natural products that include many antibiotics and anti-tumor compounds. Despite the recent advances in metabolomics analysis, still little is known about the cyclopeptides in the human gut and their possible interactions due to a lack of computational analysis pipelines that are applicable to such compounds. Here, we introduce CycloNovo, an algorithm for automated de novo cyclopeptide analysis and sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms, to identify cyclopeptides in spectral datasets. CycloNovo reconstructed 32 previously unreported cyclopeptides (to the best of our knowledge) in the human gut and reported over a hundred cyclopeptides in other environments represented by various spectra on Global Natural Products Social Molecular Network (GNPS). https://github.com/bbehsaz/cyclonovo.
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17
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Liu X, Wang Z, Zhang J, Song L, Li D, Wu Z, Zhu B, Nakamura Y, Shahidi F, Yu C, Zhou D. Isolation and identification of zinc-chelating peptides from sea cucumber (Stichopus japonicus) protein hydrolysate. J Sci Food Agric 2019; 99:6400-6407. [PMID: 31283025 DOI: 10.1002/jsfa.9919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Zinc is known to play an essential role in the biological activities in the human body. In this study, a zinc-chelating peptide (ZCP) produced by Alcalase-assisted hydrolysis of the body wall of sea cucumber was isolated and identified. The ZCP was purified stepwise by ultrafiltration, anion-exchange chromatography, and gel filtration chromatography, in conjunction with ultraviolet-visual (UV-visual) spectrophotometry, which was used to analyze each purified fraction. RESULTS Analysis of the purified ZCP revealed that its zinc-chelating ability was 33.31%. Analysis of isothermal titration calorimetry suggested that the binding of ZCP and zinc (N ≈ 2) was endothermic, with weak binding affinity. Fourier transform infrared spectroscopy spectra (FTIR) indicated that carboxylic and amide groups in ZCP were the primary binding sites of Zn. Sequencing the result by ultra-performance liquid chromatography-quadrupole/time of flight mass spectrometry (UPLC-Q-TOF-MS/MS) showed that a representative ZCP had the sequence WLTPTYPE with a molecular weight of 1005.5 Da. CONCLUSION These results provide a promising foundation for the production of zinc supplements from sea-cucumber-derived ZCPs. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Xiaoyang Liu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- National Engineering Research Center of Seafood, Dalian, China
| | - Zixu Wang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- National Engineering Research Center of Seafood, Dalian, China
| | - Jing Zhang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- National Engineering Research Center of Seafood, Dalian, China
| | - Liang Song
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- National Engineering Research Center of Seafood, Dalian, China
| | - Deyang Li
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- National Engineering Research Center of Seafood, Dalian, China
| | - Zixuan Wu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- National Engineering Research Center of Seafood, Dalian, China
| | - Beiwei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- National Engineering Research Center of Seafood, Dalian, China
| | - Yoshimasa Nakamura
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Fereidoon Shahidi
- Department of Biochemistry, Memorial University of Newfoundland, St John's, NL, Canada
| | - Chenxu Yu
- National Engineering Research Center of Seafood, Dalian, China
- Department of Agricultural and Biosystems Engineering, Iowa State University, Iowa, USA
| | - Dayong Zhou
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
- National Engineering Research Center of Seafood, Dalian, China
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Callahan N, Tullman J, Kelman Z, Marino J. Strategies for Development of a Next-Generation Protein Sequencing Platform. Trends Biochem Sci 2019; 45:76-89. [PMID: 31676211 DOI: 10.1016/j.tibs.2019.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 02/08/2023]
Abstract
Proteomic analysis can be a critical bottleneck in cellular characterization. The current paradigm relies primarily on mass spectrometry of peptides and affinity reagents (i.e., antibodies), both of which require a priori knowledge of the sample. An unbiased protein sequencing method, with a dynamic range that covers the full range of protein concentrations in proteomes, would revolutionize the field of proteomics, allowing a more facile characterization of novel gene products and subcellular complexes. To this end, several new platforms based on single-molecule protein-sequencing approaches have been proposed. This review summarizes four of these approaches, highlighting advantages, limitations, and challenges for each method towards advancing as a core technology for next-generation protein sequencing.
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Affiliation(s)
- Nicholas Callahan
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA.
| | - Jennifer Tullman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA; Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
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Danquah BD, Röwer C, Opuni KM, El-Kased R, Frommholz D, Illges H, Koy C, Glocker MO. Intact Transition Epitope Mapping - Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE). Mol Cell Proteomics 2019; 18:1543-1555. [PMID: 31147491 PMCID: PMC6683010 DOI: 10.1074/mcp.ra119.001429] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Epitope mapping, which is the identification of antigenic determinants, is essential for the design of novel antibody-based therapeutics and diagnostic tools. ITEM-THREE is a mass spectrometry-based epitope mapping method that can identify epitopes on antigens upon generating an immune complex in electrospray-compatible solutions by adding an antibody of interest to a mixture of peptides from which at least one holds the antibody's epitope. This mixture is nano-electrosprayed without purification. Identification of the epitope peptide is performed within a mass spectrometer that provides an ion mobility cell sandwiched in-between two collision cells and where this ion manipulation setup is flanked by a quadrupole mass analyzer on one side and a time-of-flight mass analyzer on the other side. In a stepwise fashion, immune-complex ions are separated from unbound peptide ions and dissociated to release epitope peptide ions. Immune complex-released peptide ions are separated from antibody ions and fragmented by collision induced dissociation. Epitope-containing peptide fragment ions are recorded, and mass lists are submitted to unsupervised data base search thereby retrieving both, the amino acid sequence of the epitope peptide and the originating antigen. ITEM-THREE was developed with antiTRIM21 and antiRA33 antibodies for which the epitopes were known, subjecting them to mixtures of synthetic peptides of which one contained the respective epitope. ITEM-THREE was then successfully tested with an enzymatic digest of His-tagged recombinant human β-actin and an antiHis-tag antibody, as well as with an enzymatic digest of recombinant human TNFα and an antiTNFα antibody whose epitope was previously unknown.
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Affiliation(s)
- Bright D Danquah
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Claudia Röwer
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | - Reham El-Kased
- ¶Microbiology and Immunology Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - David Frommholz
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany
| | - Harald Illges
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany;; **University of Applied Sciences Bonn-Rhein-Sieg, Institute for Functional Gene Analytics, Rheinbach, Germany
| | - Cornelia Koy
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Michael O Glocker
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany.
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20
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Kim M, Park JM, Yun TG, Noh JY, Kang MJ, Pyun JC. TiO 2 Nanowires from Wet-Corrosion Synthesis for Peptide Sequencing Using Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. ACS Appl Mater Interfaces 2018; 10:33790-33802. [PMID: 30212181 DOI: 10.1021/acsami.8b03804] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this work, TiO2 nanowires synthesized from a wet-corrosion process were presented for peptide sequencing by photocatalytic reaction with UV radiation. For the photocatalytic decomposition of peptides, the peptide sample was dropped on a target plate containing synthesized TiO2 nanowire zones and UV-irradiated. Subsequently, the target plate was analyzed by laser desorption/ionization time-of-flight (LDI-TOF) mass spectrometry using the synthesized TiO2 nanowires as a solid matrix. The feasibility of peptide sequencing based on the photocatalytic reaction with the synthesized TiO2 nanowires was demonstrated using six types of peptides GHP9 (G1-H-P-Q-G2-K1-K2-K3-K4, 1006.59 Da), BPA-1(K1-S1-L-E-N-S2-Y-G1-G2-G3-K2-K3-K4, 1394.74 Da), PreS1(F1-G-A-N1-S-N2-N3-P1-D1-W-D2-F2-N4-P2-N5, 1707.68 Da), HPQ peptide-1 (G-Y-H-P-Q-R-K, 884.45 Da), HPQ peptide-2 (K-R-H-P-Q-Y-G, 884.45 Da), and HPQ peptide-3 (R-Y-H-P-Q-G-K, 884.45 Da). The identification of three different peptides with the same molecular weight was also demonstrated by using the synthesized TiO2 nanowires for their photocatalytic decomposition as well as for LDI-TOF mass spectrometry as a solid-matrix.
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Affiliation(s)
- Mira Kim
- Department of Materials Science and Engineering , Yonsei University , 134 Shinchon-dong , Seodaemun-gu, Seoul 03722 , Korea
| | - Jong-Min Park
- Department of Materials Science and Engineering , Yonsei University , 134 Shinchon-dong , Seodaemun-gu, Seoul 03722 , Korea
| | - Tae Gyeong Yun
- Department of Materials Science and Engineering , Yonsei University , 134 Shinchon-dong , Seodaemun-gu, Seoul 03722 , Korea
| | - Joo-Yoon Noh
- Department of Materials Science and Engineering , Yonsei University , 134 Shinchon-dong , Seodaemun-gu, Seoul 03722 , Korea
| | - Min-Jung Kang
- Korea Institute of Science and Technology (KIST) , Seoul 02792 , Korea
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering , Yonsei University , 134 Shinchon-dong , Seodaemun-gu, Seoul 03722 , Korea
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21
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Abstract
As a popular sample preparation approach, filter-aided sample preparation (FASP) has been widely used in proteomic analysis. However, several limitations have been noted, including sample loss during filtration, repetitive centrifugation steps, and the possibility of breakage of filtration membrane. Extraction bias among different sample preparation strategies presents another challenge. To overcome these limitations and address remaining challenges, we developed a novel surfactant and chaotropic agent assisted sequential extraction/on-pellet digestion (SCAD) protocol. The new strategy resulted in higher protein yield and improved peptide recovery and protein coverage compared to two conventional sample preparation methods (FASP and urea). In combination of three strategies, more than 10,000 distinct protein groups were identified with 1% FDR from MDA-MB-231 cells without any prefractionation. This in-depth proteome analysis was accomplished by optimization of protein extraction, enzymatic digestion, LC gradient, and peptide sequencing method. Ingenuity Pathways Analysis (IPA) of proteins exclusively identified in SCAD revealed several crucial signaling pathways that regulate breast cancer progression. SCAD also enabled an unbiased extraction of different categories of proteins (membrane, intracellular, nuclear) associated with tumorigenesis, which integrates the advantages of FASP and urea extraction. This novel strategy expedites comprehensive protein identification, which is applicable for biomarker discovery in various types of cancers.
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Affiliation(s)
- Fengfei Ma
- School of Pharmacy, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
| | - Fabao Liu
- McArdle Laboratory for Cancer Research, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin‒Madison, Madison, Wisconsin 53706, United States
- School of Life Sciences, Tianjin University, Tianjin 300072, P. R. China
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22
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Setner B, Stefanowicz P, Szewczuk Z. Quaternary ammonium isobaric tag for a relative and absolute quantification of peptides. J Mass Spectrom 2018; 53:115-123. [PMID: 29087004 DOI: 10.1002/jms.4040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/11/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
Isobaric labeling quantification of peptides has become a method of choice for mass spectrometry-based proteomics studies. However, despite of wide variety of commercially available isobaric tags, none of the currently available methods offers significant improvement of sensitivity of detection during MS experiment. Recently, many strategies were applied to increase the ionization efficiency of peptides involving chemical modifications introducing quaternary ammonium fixed charge. Here, we present a novel quaternary ammonium-based isobaric tag for relative and absolute quantification of peptides (QAS-iTRAQ 2-plex). Upon collisional activation, the new stable benzylic-type cationic reporter ion is liberated from the tag. Deuterium atoms were used to offset the differential masses of a reporter group. We tested the applicability of QAS-iTRAQ 2-plex reagent on a series of model peptides as well as bovine serum albumin tryptic digest. Obtained results suggest usefulness of this isobaric ionization tag for relative and absolute quantification of peptides.
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Affiliation(s)
- Bartosz Setner
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław, 50-383, Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław, 50-383, Poland
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław, 50-383, Poland
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23
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Díez P, Ibarrola N, Dégano RM, Lécrevisse Q, Rodriguez-Caballero A, Criado I, Nieto WG, Góngora R, González M, Almeida J, Orfao A, Fuentes M. A systematic approach for peptide characterization of B-cell receptor in chronic lymphocytic leukemia cells. Oncotarget 2017; 8:42836-42846. [PMID: 28467808 PMCID: PMC5522109 DOI: 10.18632/oncotarget.17076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/22/2017] [Indexed: 01/09/2023] Open
Abstract
A wide variety of immunoglobulins (Ig) is produced by the immune system thanks to different mechanisms (V(D)J recombination, somatic hypermutation, and antigen selection). The profiling of Ig sequences (at both DNA and peptide levels) are of great relevance to developing targeted vaccines or treatments for specific diseases or infections. Thus, genomics and proteomics techniques (such as Next-Generation Sequencing (NGS) and mass spectrometry (MS)) have notably increased the knowledge in Ig sequencing and serum Ig peptide profiling in a high-throughput manner. However, the peptide characterization of membrane-bound Ig (e.g., B-cell receptors, BCR) is still a challenge mainly due to the poor recovery of mentioned Ig.Herein, we have evaluated three different sample processing methods for peptide sequencing of BCR belonging to chronic lymphocytic leukemia (CLL) B cells identifying up to 426 different peptide sequences (MS/MS data are available via ProteomeXchange with identifier PXD004466). Moreover, as a consequence of the results here obtained, recommended guidelines have been described for BCR-sequencing of B-CLL samples by MS approaches.For this purpose, an in-house algorithm has been designed and developed to compare the MS/MS results with those obtained by molecular biology in order to integrate both proteomics and genomics results and establish the steps to follow when sequencing membrane-bound Ig by MS/MS.
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MESH Headings
- Aged
- Aged, 80 and over
- Amino Acid Sequence
- Female
- Genomics/methods
- High-Throughput Nucleotide Sequencing
- Humans
- Immunoglobulin Heavy Chains/chemistry
- Immunoglobulin Heavy Chains/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Male
- Middle Aged
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Proteomics/methods
- Receptors, Antigen, B-Cell/chemistry
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Tandem Mass Spectrometry
- Workflow
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Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Nieves Ibarrola
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Rosa M. Dégano
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Quentin Lécrevisse
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Arancha Rodriguez-Caballero
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Ignacio Criado
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Wendy G. Nieto
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Marcos González
- Hematology Service, Institute of Biomedical Research of Salamanca, University Hospital of Salamanca, Cancer Research and Institute of Molecular Biology and Cellular Oncology, 37007 Salamanca, Spain
| | - Julia Almeida
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
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24
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Wither MJ, Hansen KC, Reisz JA. Mass Spectrometry-Based Bottom-Up Proteomics: Sample Preparation, LC-MS/MS Analysis, and Database Query Strategies. ACTA ACUST UNITED AC 2016; 86:16.4.1-16.4.20. [PMID: 27801520 DOI: 10.1002/cpps.18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recent technological advances in mass spectrometry (MS) have made possible the investigation and quantification of complex mixtures of biomolecules. The exceptional sensitivity and resolving power of today's mass spectrometers allow for the detection of proteins and peptides at low femtomole quantities; however, these attributes demand high sample purity to minimize artifacts and achieve the highest degree of biomolecule identification. Tissue preparation for proteomic studies is particularly challenging due to their heterogeneity in cell type, presence of insoluble biomaterials, and wide diversity of biomolecules. The workflow described herein details sample preparation from tissues through protein extraction, proteolysis, and purification to generate peptides for MS analysis. Increased peptide resolution and a corresponding increase in protein identification is accomplished using polarity-based fractionation (C18 resin) at the peptide level. Additionally, approaches to instrument set up, including the use of nanoscale liquid chromatography and quadrupole Orbitrap MS, along with database searching, are described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Matthew J Wither
- Biological Mass Spectrometry Core, Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Kirk C Hansen
- Biological Mass Spectrometry Core, Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Julie A Reisz
- Biological Mass Spectrometry Core, Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
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25
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Meier F, Beck S, Grassl N, Lubeck M, Park MA, Raether O, Mann M. Parallel Accumulation-Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device. J Proteome Res 2015; 14:5378-87. [PMID: 26538118 DOI: 10.1021/acs.jproteome.5b00932] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In liquid chromatography-mass spectrometry (LC-MS)-based proteomics, many precursors elute from the column simultaneously. In data-dependent analyses, these precursors are fragmented one at a time, whereas the others are discarded entirely. Here we employ trapped ion mobility spectrometry (TIMS) on an orthogonal quadrupole time-of-flight (QTOF) mass spectrometer to remove this limitation. In TIMS, all precursor ions are accumulated in parallel and released sequentially as a function of their ion mobility. Instead of selecting a single precursor mass with the quadrupole mass filter, we here implement synchronized scans in which the quadrupole is mass positioned with sub-millisecond switching times at the m/z values of appropriate precursors, such as those derived from a topN precursor list. We demonstrate serial selection and fragmentation of multiple precursors in single 50 ms TIMS scans. Parallel accumulation-serial fragmentation (PASEF) enables hundreds of MS/MS events per second at full sensitivity. Modeling the effect of such synchronized scans for shotgun proteomics, we estimate that about a 10-fold gain in sequencing speed should be achievable by PASEF without a decrease in sensitivity.
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Affiliation(s)
- Florian Meier
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Scarlet Beck
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Niklas Grassl
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Markus Lubeck
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Melvin A Park
- Bruker Daltonics Inc., 40 Manning Road, Billerica, Massachusetts 01821, United States
| | - Oliver Raether
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Matthias Mann
- Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
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26
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Setner B, Rudowska M, Klem E, Cebrat M, Szewczuk Z. Peptides derivatized with bicyclic quaternary ammonium ionization tags. Sequencing via tandem mass spectrometry. J Mass Spectrom 2014; 49:995-1001. [PMID: 25303389 DOI: 10.1002/jms.3410] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/28/2014] [Accepted: 06/06/2014] [Indexed: 06/04/2023]
Abstract
Improving the sensitivity of detection and fragmentation of peptides to provide reliable sequencing of peptides is an important goal of mass spectrometric analysis. Peptides derivatized by bicyclic quaternary ammonium ionization tags: 1-azabicyclo[2.2.2]octane (ABCO) or 1,4-diazabicyclo[2.2.2]octane (DABCO), are characterized by an increased detection sensitivity in electrospray ionization mass spectrometry (ESI-MS) and longer retention times on the reverse-phase (RP) chromatography columns. The improvement of the detection limit was observed even for peptides dissolved in 10 mM NaCl. Collision-induced dissociation tandem mass spectrometry of quaternary ammonium salts derivatives of peptides showed dominant a- and b-type ions, allowing facile sequencing of peptides. The bicyclic ionization tags are stable in collision-induced dissociation experiments, and the resulted fragmentation pattern is not significantly influenced by either acidic or basic amino acid residues in the peptide sequence. Obtained results indicate the general usefulness of the bicyclic quaternary ammonium ionization tags for ESI-MS/MS sequencing of peptides.
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Affiliation(s)
- Bartosz Setner
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
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27
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Cydzik M, Rudowska M, Stefanowicz P, Szewczuk Z. The competition of charge remote and charge directed fragmentation mechanisms in quaternary ammonium salt derivatized peptides--an isotopic exchange study. J Am Soc Mass Spectrom 2011; 22:2103-7. [PMID: 21972014 PMCID: PMC3220814 DOI: 10.1007/s13361-011-0245-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 08/26/2011] [Accepted: 08/31/2011] [Indexed: 05/12/2023]
Abstract
Derivatization of peptides as quaternary ammonium salts (QAS) is a promising method for sensitive detection by electrospray ionization tandem mass spectrometry (Cydzik et al. J. Pept. Sci. 2011, 17, 445-453). The peptides derivatized by QAS at their N-termini undergo fragmentation according to the two competing mechanisms - charge remote (ChR) and charge directed (ChD). The absence of mobile proton in the quaternary salt ion results in ChR dissociation of a peptide bond. However, Hofmann elimination of quaternary salt creates an ion with one mobile proton leading to the ChD fragmentation. The experiments on the quaternary ammonium salts with deuterated N-alkyl groups or amide NH bonds revealed that QAS derivatized peptides dissociate according to the mixed ChR-ChD mechanism. The isotopic labeling allows differentiation of fragments formed according to ChR and ChD mechanisms.
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Affiliation(s)
- Marzena Cydzik
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Magdalena Rudowska
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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28
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Li X, Huang Y, O’Connor PB, Lin C. Structural heterogeneity of doubly-charged peptide b-ions. J Am Soc Mass Spectrom 2011; 22:245-54. [PMID: 21472584 PMCID: PMC3305756 DOI: 10.1007/s13361-010-0036-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 11/09/2010] [Accepted: 11/11/2010] [Indexed: 05/30/2023]
Abstract
Performing collisionally activated dissociation (CAD) and electron capture dissociation (ECD) in tandem has shown great promise in providing comprehensive sequence information that was otherwise unobtainable by using either fragmentation method alone or in duet. However, the general applicability of this MS(3) approach in peptide sequencing may be undermined by the formation of non-direct sequence ions, as sometimes observed under CAD, particularly when multiple stages of CAD are involved. In this study, varied-sized doubly-charged b-ions from three tachykinin peptides were investigated by ECD. Sequence scrambling was observed in ECD of all b-ions from neurokinin A (HKTDSFVGLM-NH(2)), suggesting the presence of N- and C-termini linked macro-cyclic conformers. On the contrary, none of the b-ions from eledoisin (pEPSKDAFIGLM-NH(2)) produced non-direct sequence ions under ECD, as it does not contain a free N-terminal amino group. ECD of several b-ions from Substance P (RPKPQQFFGLM-NH(2)) showed series of c(m)-Lys fragment ions which suggested that the macro-cyclic structure may also be formed by connecting the C-terminal carbonyl group and the ε-amino group of the lysine side chain. Theoretical investigation of selected Substance P b-ions revealed several low energy conformers, including both linear oxazolones and macro-ring structures, in corroboration with the experimental observation. This study showed that a b-ion may exist as a mixture of several forms, with their propensities influenced by its N-terminus, length, and certain side-chain groups. Further, the presence of several macro-cyclic structures may result in erroneous sequence assignment when the combined CAD and ECD methods are used in peptide sequencing.
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Affiliation(s)
- Xiaojuan Li
- Mass Spectrometry Resource, Department of Biochemistry, School of Medicine, Boston University, Boston, MA, USA
| | - Yiqun Huang
- Mass Spectrometry Resource, Department of Biochemistry, School of Medicine, Boston University, Boston, MA, USA
| | - Peter B. O’Connor
- Mass Spectrometry Resource, Department of Biochemistry, School of Medicine, Boston University, Boston, MA, USA
- Department of Chemistry, the University of Warwick, Coventry, UK
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, School of Medicine, Boston University, Boston, MA, USA
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29
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Krivos KL, Limbach PA. Sequence analysis of peptide:oligonucleotide heteroconjugates by electron capture dissociation and electron transfer dissociation. J Am Soc Mass Spectrom 2010; 21:1387-1397. [PMID: 20435485 PMCID: PMC3638748 DOI: 10.1016/j.jasms.2010.03.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 03/30/2010] [Accepted: 03/30/2010] [Indexed: 05/29/2023]
Abstract
Mass spectrometry analysis of protein-nucleic acid cross-links is challenging due to the dramatically different chemical properties of the two components. Identifying specific sites of attachment between proteins and nucleic acids requires methods that enable sequencing of both the peptide and oligonucleotide component of the heteroconjugate cross-link. While collision-induced dissociation (CID) has previously been used for sequencing such heteroconjugates, CID generates fragmentation along the phosphodiester backbone of the oligonucleotide preferentially. The result is a reduction in peptide fragmentation within the heteroconjugate. In this work, we have examined the effectiveness of electron capture dissociation (ECD) and electron-transfer dissociation (ETD) for sequencing heteroconjugates. Both methods were found to yield preferential fragmentation of the peptide component of a peptide:oligonucleotide heteroconjugate, with minimal differences in sequence coverage between these two electron-induced dissociation methods. Sequence coverage was found to increase with increasing charge state of the heteroconjugate, but decreases with increasing size of the oligonucleotide component. To overcome potential intermolecular interactions between the two components of the heteroconjugate, supplemental activation with ETD was explored. The addition of a supplemental activation step was found to increase peptide sequence coverage over ETD alone, suggesting that electrostatic interactions between the peptide and oligonucleotide components are one limiting factor in sequence coverage by these two approaches. These results show that ECD/ETD methods can be used for the tandem mass spectrometry sequencing of peptide:oligonucleotide heteroconjugates, and these methods are complementary to existing CID methods already used for sequencing of protein-nucleic acid cross-links.
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Affiliation(s)
| | - Patrick A. Limbach
- To whom correspondence should be addressed. Phone (513) 556-1871, Fax (513) 556-9239,
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30
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Abstract
In previous papers, we highlighted the role of ammonium sulfate in increasing peptide fragmentation by in-source decay (ISD). The current work systematically investigated effects of matrix assisted laser desorption ionization (MALDI) extraction delay, peptide amino acid composition, matrix, and ammonium sulfate concentration on peptide ISD fragmentation. The data confirmed that ammonium sulfate increased peptides signal-to-noise ratio as well as their in-source fragmentation, resulting in complete sequence coverage regardless of the amino acid composition. This method is easy, inexpensive, and generates the peptides sequence instantly.
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31
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Ma M, Szabo TM, Jia C, Marder E, Li L. Mass spectrometric characterization and physiological actions of novel crustacean C-type allatostatins. Peptides 2009; 30:1660-8. [PMID: 19505516 PMCID: PMC2721915 DOI: 10.1016/j.peptides.2009.05.023] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 05/25/2009] [Accepted: 05/27/2009] [Indexed: 11/26/2022]
Abstract
The crustacean stomatogastric ganglion (STG) is modulated by numerous neuropeptides that are released locally in the neuropil or that reach the STG as neurohormones. Using 1,5-diaminonaphthalene (DAN) as a reductive screening matrix for matrix-assisted laser desorption/ionization (MALDI) mass spectrometric profiling of disulfide bond-containing C-type allatostatin peptides followed by electrospray ionization quadrupole time-of-flight (ESI-Q-TOF) tandem mass spectrometric (MS/MS) analysis, we identified and sequenced a novel C-type allatostatin peptide (CbAST-C1), pQIRYHQCYFNPISCF-COOH, present in the pericardial organs of the crab, Cancer borealis. Another C-type allatostatin (CbAST-C2), SYWKQCAFNAVSCFamide, was discovered using the expressed sequence tag (EST) database search strategy in both C. borealis and the lobster, Homarus americanus, and further confirmed with de novo sequencing using ESI-Q-TOF tandem MS. Electrophysiological experiments demonstrated that both CbAST-C1 and CbAST-C2 inhibited the frequency of the pyloric rhythm of the STG, in a state-dependent manner. At 10(-6)M, both peptides were only modestly effective when initial frequencies of the pyloric rhythm were >0.8Hz, but almost completely suppressed the pyloric rhythm when applied to preparations with starting frequencies <0.7Hz. Surprisingly, these state-dependent actions are similar to those of the structurally unrelated allatostatin A and allatostatin B families of peptides.
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Affiliation(s)
- Mingming Ma
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Theresa M. Szabo
- Volen Center and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Chenxi Jia
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Eve Marder
- Volen Center and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Address correspondence and reprint requests to Dr Lingjun Li, School of Pharmacy, University of Wisconsin, 777 Highland Ave., Madison, WI 53705-2222, USA. E-mail: . Phone: (608)265-8491, Fax: (608)262-5345
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Ma M, Bors EK, Dickinson ES, Kwiatkowski MA, Sousa GL, Henry RP, Smith CM, Towle DW, Christie AE, Li L. Characterization of the Carcinus maenas neuropeptidome by mass spectrometry and functional genomics. Gen Comp Endocrinol 2009; 161:320-34. [PMID: 19523386 PMCID: PMC2888039 DOI: 10.1016/j.ygcen.2009.01.015] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 12/15/2008] [Accepted: 01/20/2009] [Indexed: 11/19/2022]
Abstract
Carcinus maenas, commonly known as the European green crab, is one of the best-known and most successful marine invasive species. While a variety of natural and anthropogenic mechanisms are responsible for the geographic spread of this crab, its ability to adapt physiologically to a broad range of salinities, temperatures and other environmental factors has enabled its successful establishment in new habitats. To extend our understanding of hormonal control in C. maenas, including factors that allow for its extreme adaptability, we have undertaken a mass spectral/functional genomics investigation of the neuropeptides used by this organism. Via a strategy combining MALDI-based high resolution mass profiling, biochemical derivatization, and nanoscale separation coupled to tandem mass spectrometric sequencing, 122 peptide paracrines/hormones were identified from the C. maenas central nervous system and neuroendocrine organs. These peptides include 31 previously described Carcinus neuropeptides (e.g. NSELINSILGLPKVMNDAamide [beta-pigment dispersing hormone] and PFCNAFTGCamide [crustacean cardioactive peptide]), 49 peptides only described in species other than the green crab (e.g. pQTFQYSRGWTNamide [Arg(7)-corazonin]), and 42 new peptides de novo sequenced here for the first time (e.g. the pyrokinins TSFAFSPRLamide and DTGFAFSPRLamide). Of particular note are large collections of FMRFamide-like peptides (25, including nine new isoforms sequenced de novo) and A-type allatostatin peptides (25, including 10 new sequences reported here for the first time) in this study. Also of interest is the identification of two SIFamide isoforms, GYRKPPFNGSIFamide and VYRKPPFNGSIFamide, the latter peptide known previously only from members of the astacidean genus Homarus. Using transcriptome analyses, 15 additional peptides were characterized, including an isoform of bursicon beta and a neuroparsin-like peptide. Collectively, the data presented in this study not only greatly expand the number of identified C. maenas neuropeptides, but also provide a framework for future investigations of the physiological roles played by these molecules in this highly adaptable species.
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Affiliation(s)
- Mingming Ma
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705-2222 USA
| | - Eleanor K. Bors
- Center for Marine Functional Genomics, Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, Maine 04672 USA
| | - Evelyn S. Dickinson
- Center for Marine Functional Genomics, Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, Maine 04672 USA
| | - Molly A. Kwiatkowski
- Center for Marine Functional Genomics, Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, Maine 04672 USA
| | - Gregory L. Sousa
- Center for Marine Functional Genomics, Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, Maine 04672 USA
| | - Raymond P. Henry
- Deparment of Biological Sciences, Auburn University, 101 Life Sciences Building, Auburn, Alabama 36849 USA
| | - Christine M. Smith
- Center for Marine Functional Genomics, Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, Maine 04672 USA
| | - David W. Towle
- Center for Marine Functional Genomics, Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, Maine 04672 USA
| | - Andrew E. Christie
- Center for Marine Functional Genomics, Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, Maine 04672 USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705-2222 USA
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706-1396 USA
- Correspondence to: Dr. Lingjun Li, School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705-2222 USA; Phone: 608-265-8491; Fax: 608-262-5345;
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Abstract
Oxidative modification to the side chain of histidine can noticeably change the collision-induced dissociation (CID) pathways of peptides containing this oxidized residue. In cases where an oxidized peptide consists two or more isomers differing only in the site of modification, oxidation to histidine usually causes the other oxidized sites to be mis-assigned in CID spectra. These spectral misassignments can sometimes be avoided by using multiple stages of MS/MS (MS(n)) or via specially optimized liquid chromatographic separation conditions. In this manuscript, we demonstrate that these misassignments can be more readily and easily avoided by using electron-transfer dissociation (ETD) to dissociate the oxidized peptides. Furthermore, we find that the relative insensitivity of ETD to side-chain chemistry allows the extent of oxidative modification to be determined readily for peptide isomers having more than one site of oxidation. The current results along with previous studies of oxidized peptides suggest that ETD is probably a better technique than CID for obtaining correct sequence and modification information for oxidized peptides.
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Affiliation(s)
- Rapole Srikanth
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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Ma M, Chen R, Sousa GL, Bors EK, Kwiatkowski M, Goiney CC, Goy MF, Christie AE, Li L. Mass spectral characterization of peptide transmitters/hormones in the nervous system and neuroendocrine organs of the American lobster Homarus americanus. Gen Comp Endocrinol 2008; 156:395-409. [PMID: 18304551 PMCID: PMC2293973 DOI: 10.1016/j.ygcen.2008.01.009] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Revised: 12/08/2007] [Accepted: 01/04/2008] [Indexed: 10/22/2022]
Abstract
The American lobster Homarus americanus is a decapod crustacean with both high economic and scientific importance. To facilitate physiological investigations of peptide transmitter/hormone function in this species, we have used matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and nanoscale liquid chromatography coupled to electrospray ionization quadrupole time-of-flight tandem mass spectrometry (nanoLC-ESI-Q-TOF MS/MS) to elucidate the peptidome present in its nervous system and neuroendocrine organs. In total, 84 peptides were identified, including 27 previously known H. americanus peptides (e.g., VYRKPPFNGSIFamide [Val(1)-SIFamide]), 23 peptides characterized previously from other decapods, but new to the American lobster (e.g., pQTFQYSRGWTNamide [Arg(7)-corazonin]), and 34 new peptides de novo sequenced/detected for the first time in this study. Of particular note are a novel B-type allatostatin (TNWNKFQGSWamide) and several novel FMRFamide-related peptides, including an unsulfated analog of sulfakinin (GGGEYDDYGHLRFamide), two myosuppressins (QDLDHVFLRFamide and pQDLDHVFLRFamide), and a collection of short neuropeptide F isoforms (e.g., DTSTPALRLRFamide and FEPSLRLRFamide). Our data also include the first detection of multiple tachykinin-related peptides in a non-brachyuran decapod, as well as the identification of potential individual-specific variants of orcokinin and orcomyotropin-related peptide. Taken collectively, our results not only expand greatly the number of known H. americanus neuropeptides, but also provide a framework for future studies on the physiological roles played by these molecules in this commercially and scientifically important species.
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Affiliation(s)
- Mingming Ma
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705-2222 USA
| | - Ruibing Chen
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706-1396 USA
| | - Gregory L. Sousa
- Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, Maine 04672 USA
| | - Eleanor K. Bors
- Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, Maine 04672 USA
| | - Molly Kwiatkowski
- Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, Maine 04672 USA
| | - Christopher C. Goiney
- Department of Biology, University of Washington, Box 351800, Seattle, Washington 98195-1800 USA
| | - Michael F. Goy
- Department of Cell and Molecular Physiology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 USA
| | - Andrew E. Christie
- Mount Desert Island Biological Laboratory, P.O. Box 35, Old Bar Harbor Road, Salisbury Cove, Maine 04672 USA
- Department of Biology, University of Washington, Box 351800, Seattle, Washington 98195-1800 USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705-2222 USA
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706-1396 USA
- Correspondence to: Dr. Lingjun Li, School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705-2222 USA; Phone: 608-265-8491; Fax: 608-262-5345;
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Wilson JJ, Kirkovits GJ, Sessler JL, Brodbelt JS. Photodissociation of non-covalent peptide-crown ether complexes. J Am Soc Mass Spectrom 2008; 19:257-60. [PMID: 18077179 PMCID: PMC2288744 DOI: 10.1016/j.jasms.2007.10.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 10/29/2007] [Accepted: 10/29/2007] [Indexed: 05/25/2023]
Abstract
Highly chromogenic 18-crown-6-dipyrrolylquinoxaline coordinates primary amines of peptides, forming non-covalent complexes that can be transferred to the gas-phase by electrospray ionization. The appended chromogenic crown ether facilitates efficient energy transfer to the peptide upon ultraviolet irradiation in the gas phase, resulting in diagnostic peptide fragmentation. Collisional-activated dissociation and infrared multiphoton dissociation of these non-covalent complexes result only in their disassembly with the charge retained on either the peptide or crown ether, yielding no sequence ions. Upon UV photon absorption the intermolecular energy transfer is facilitated by the fast activation timescale of ultraviolet photodissociation (<10 ns) and by the collectively strong hydrogen bonding between the crown ether and peptide, thus allowing effective transfer of energy to the peptide moiety before disruption of the intermolecular hydrogen bonds.
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Affiliation(s)
- Jeffrey J Wilson
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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Conrotto P, Hellman U. Sulfonation chemistry as a powerful tool for MALDI TOF/TOF de novo sequencing and post-translational modification analysis. J Biomol Tech 2005; 16:441-52. [PMID: 16522867 PMCID: PMC2291740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Mass spectrometry using matrix-assisted laser desorption/ionization (MALDI) is a widespread technique for various types of proteomic analysis. In the identification of proteins using peptide mass fingerprinting, samples are enzymatically digested and resolved into a number of peptides, whose masses are determined and matched with a sequence data-base. However, the presence inside the cell of several splicing variants, protein isoforms, or fusion proteins gives rise to a complex picture, demanding more complete analysis. Moreover, the study of species with yet uncharacterized genomes or the investigation of post-translational modifications are not possible with classical mass fingerprinting, and require specific and accurate de novo sequencing. In the last several years, much effort has been made to improve the performance of peptide sequencing with MALDI. Here we present applications using a fast and robust chemical modification of peptides for improved de novo sequencing. Post-source decay of derivatized peptides generates at the same time peaks with high intensity and simple spectra, leading to a very easy and clear sequence determination.
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Abstract
Ion channels activated by the binding of cyclic nucleotides first were discovered in retinal rods where they generate the cell's response to light. In other systems, however, it has been difficult to unambiguously determine whether cyclic nucleotide-dependent processes are mediated by protein kinases, their classical effector enzymes, or cyclic nucleotide-gated (CNG) ion channels. Part of this difficulty has been caused by the lack of specific pharmacological tools. Here we report the purification from the venom of the Australian King Brown snake of a peptide toxin that inhibits current through CNG channels. This toxin, which we have named Pseudechetoxin (PsTx), was purified by cation exchange and RP-HPLC and has a molecular mass of about 24 kDa. When applied to the extracellular face of membrane patches containing the alpha-subunit of the rat olfactory CNG channel, PsTx blocked the cGMP-dependent current with a Ki of 5 nM. Block was independent of voltage and required only a single molecule of toxin. PsTx also blocked CNG channels containing the bovine rod alpha-subunit with high affinity (100 nM), but it was less effective on the heteromeric version of the rod channel (Ki approximately 3 microM). We have obtained N-terminal and partial internal sequence data and the amino acid composition of PsTx. These data indicate that PsTx is a basic protein that exhibits some homology with helothermine, a toxin isolated from the venom of the Mexican beaded lizard. PsTx promises to be a valuable pharmacological tool for studies on the structure and physiology of CNG channels.
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Affiliation(s)
- R L Brown
- Neurological Sciences Institute, Oregon Health Sciences University, 1120 NW 20th Avenue, Portland, OR 97209, USA.
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Kobayashi H, Sato K, Miyokawa N, Kimura S, Nakashima M, Katagiri M. Analysis of naturally processed human histocompatibility leukocyte antigen class I-bound peptides from hepatocellular carcinoma tissues in vivo. Jpn J Cancer Res 1995; 86:962-8. [PMID: 7493916 PMCID: PMC5920595 DOI: 10.1111/j.1349-7006.1995.tb03008.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Naturally processed self-peptides bound to human histocompatibility leukocyte antigens (HLA) class I molecules of human hepatocellular carcinoma tissues (HLA-A2.1, -B44, -B13) in vivo were isolated for sequence analysis. Acid-eluted peptides were subjected to reversed-phase high-performance liquid chromatographic separation and single-fraction sequencing was performed by Edman degradation. The peptides were found to be octamers or nonamers and they were derived from the processing of intracellular proteins. Three independent sequences were obtained from HLA-A2.1 molecules. One of the peptides showed sequence homology to the hepatitis B virus (HBV) pre-S protein, one to aldehyde dehydrogenase, and the other to no known protein. Two independent sequences were obtained from HLA-B44, B13 molecules: one showed sequence homology to the human c-abl protein, the other showed no homology to any known protein. A synthetic biotinylated peptide based on the HBV pre-S peptide sequence was confirmed to bind to HLA-A2.1 gene-transfected L cells. These data suggested that peptides potentially recognized by cytotoxic T cells can bind to HLA class I molecules on tumor cells in vivo.
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Affiliation(s)
- H Kobayashi
- Department of Pathology, Asahikawa Medical College
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