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Rodríguez Longarela N, Paredes Ramos M, López Vilariño JM. Bioinformatics tools for the study of bioactive peptides from vegetal sources: evolution and future perspectives. Crit Rev Food Sci Nutr 2024:1-20. [PMID: 38907628 DOI: 10.1080/10408398.2024.2367571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Bioactive peptides from vegetal sources have been shown to have functional properties as anti-inflammatory, antioxidant, antihypertensive or antidiabetic capacity. For this reason, they have been proposed as an interesting and promising alternative to improve human health. In recent years, the numerous advances in the bioinformatics field for in silico prediction have speeded up the discovery of bioactive peptides, also reducing the associated costs when using an integrated approach between the classical and bioinformatics discovery. This review aims to provide an overview of the evolution, limitations and latest advances in the field of bioinformatics and computational tools, and specifically make a critical and comprehensive insight into computational techniques used to study the mechanism of interaction that allows the explanation of plant bioactive peptide functionality. In particular, molecular docking is considered key to explain the different functionalities that have been previously identified. The assumptions to simplify such a high complex environment implies a degree of uncertainty that can only be guaranteed and validated by in vitro or in vivo studies, however, the combination of databases, software and bioinformatics applications with the classical approach has become a promising procedure for the study of bioactive peptides.
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2
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Iwaniak A, Minkiewicz P, Darewicz M. Bioinformatics and bioactive peptides from foods: Do they work together? ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 108:35-111. [PMID: 38461003 DOI: 10.1016/bs.afnr.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2024]
Abstract
We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial properties, are closely interrelated. This Chapter presents the example applications of bioinformatics for studying biopeptides, focusing on main aspects of peptide analysis as the starting point, including: (i) the role of peptide databases; (ii) aspects of bioactivity prediction; (iii) simulation of peptide release from proteins. Bioinformatics can also be used for predicting other features of peptides, including ADMET, QSAR, structure, and taste. To answer the question asked "bioinformatics and bioactive peptides from foods: do they work together?", currently it is almost impossible to find examples of peptide research with no bioinformatics involved. However, theoretical predictions are not equivalent to experimental work and always require critical scrutiny. The aspects of compatibility of in silico and in vitro results are also summarized herein.
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Affiliation(s)
- Anna Iwaniak
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland.
| | - Piotr Minkiewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
| | - Małgorzata Darewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
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3
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Campanhon IB, de Aguiar PF, Bezerra FF, Soares MR, Torres AG. Human colostrum in vitro protein digestion: peptidomics by liquid chromatography-Orbitrap-high-resolution MS and prospection for bioactive peptides via bioinformatics. Br J Nutr 2024; 131:17-26. [PMID: 37485899 DOI: 10.1017/s0007114523001459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Breast milk is known to contain bioactive peptides that are released during digestion, being a major source of bioactive peptides to the new-born, some of which act against invading pathogens. However, the formation of bioactive peptides during digestion of human colostrum remains largely uninvestigated. This study aimed to investigate the formation of peptides during simulated digestion of human colostrum from adult women and to prospect antimicrobial peptides. For this purpose, we used high-resolution MS to monitor the release of peptides during in vitro digestion. Bioinformatics was used for the prospection of antimicrobial activity of peptides. During simulated digestion (oral, gastric and duodenal phases), 2318 peptide sequences derived from 112 precursor proteins were identified. At the end of simulated digestion, casein-derived peptide sequences were the most frequently observed. Among precursors, some proteins were seen for the first time in this study. The resulting peptides were rich in proline, glutamine, valine and leucine residues, providing characteristic traits of antimicrobial peptides. From bioinformatics analysis, seven peptides showed potentially high antimicrobial activity towards bacteria, viruses and fungi, from which the latter was the most prominent predicted activity. Antimicrobial peptides released during digestion may provide a defence platform with controlled release for the new-born.
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Affiliation(s)
- Isabele Batista Campanhon
- Department of Biochemistry, Institute of Chemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Lipid Biochemistry and Lipidomics Laboratory and Laboratory of Food Science and Nutritional Biochemistry, Institute of Chemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paula Fernandes de Aguiar
- Laboratory of Chemometrics (LABQUIM), Department of Analytical Chemistry, Institute of Chemistry, Universidade Federal Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flávia Fioruci Bezerra
- Department of Basic and Experimental Nutrition, Nutrition Institute, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Márcia Regina Soares
- Department of Biochemistry, Institute of Chemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Guedes Torres
- Lipid Biochemistry and Lipidomics Laboratory and Laboratory of Food Science and Nutritional Biochemistry, Institute of Chemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Leite JAS, Montoya CA, Loveday SM, Mullaney JA, Loo TS, McNabb WC, Roy NC. The impact of heating and drying on protease activities of ruminant milk before and after in vitro infant digestion. Food Chem 2023; 429:136979. [PMID: 37506658 DOI: 10.1016/j.foodchem.2023.136979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023]
Abstract
This study investigated the effect of heating (63°C/30 min or 75°C/15 s) and drying (spray-drying or freeze-drying) on plasmin, cathepsin D, and elastase activities in bovine, ovine, and caprine milk, compared to non-dried raw milk counterparts. Protease activities and protein hydrolysis were assessed before and after in vitro infant digestion with or without gastric and pancreatic enzymes. At 75°C/15 s, plasmin activity in caprine and ovine milk decreased (69-75%, p<0.05), while cathepsin D activity in spray-dried bovine milk heated increased (2.8-fold, p<0.05). Plasmin and cathepsin D activities increased (<1.2-fold, p<0.05) after in vitro digestion with pancreatin, regardless of milk species. Endogenous milk enzymes hydrolyzed more proteins than gastric enzymes during gastric digestion and contributed to small intestinal digestion. In summary, milk proteases remained active after processing with effects dependent on the species of milk, and they contributed to in vitro protein hydrolysis in the stomach and small intestine.
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Affiliation(s)
- Juliana A S Leite
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand
| | - Carlos A Montoya
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand; Smart Foods & Bioproducts Innovation Centre of Excellence, AgResearch Limited, Palmerston North 4474, New Zealand
| | - Simon M Loveday
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand; Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Jane A Mullaney
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand; High-Value Nutrition National Science Challenge, Auckland 1010, New Zealand
| | - Trevor S Loo
- School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Warren C McNabb
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand; High-Value Nutrition National Science Challenge, Auckland 1010, New Zealand
| | - Nicole C Roy
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand; High-Value Nutrition National Science Challenge, Auckland 1010, New Zealand; Department of Nutrition, University of Otago, Dunedin 9016, New Zealand.
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5
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Ning J, Yang M, Liu W, Luo X, Yue X. Proteomics and Peptidomics As a Tool to Compare the Proteins and Endogenous Peptides in Human, Cow, and Donkey Milk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16435-16451. [PMID: 37882656 DOI: 10.1021/acs.jafc.3c04534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
Cow's milk is the most widely used ingredient in infant formulas. However, its specific protein composition can cause allergic reactions. Finding alternatives to replace cow's milk and fill the nutritional gap with human milk is essential for the health of infants. Proteomic and peptidomic techniques have supported the elucidation of milk's nutritional ingredients. Recently, omics approaches have attracted increasing interest in the investigation of milk because of their high throughput, precision, sensitivity, and reproducibility. This review offers a significant overview of recent developments in proteomics and peptidomics used to study the differences in human, cow, and donkey milk. All three types of milks were identified to have critical biological functions in human health, particularly in infants. Donkey milk proteins were closer in composition to human milk, were less likely to cause allergic reactions, and may be developed as novel raw materials for formula milk powders.
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Affiliation(s)
- Jianting Ning
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Mei Yang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Wanting Liu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Xue Luo
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
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Thesbjerg MN, Nielsen SDH, Sundekilde UK, Poulsen NA, Larsen LB. Fingerprinting of Proteases, Protease Inhibitors and Indigenous Peptides in Human Milk. Nutrients 2023; 15:4169. [PMID: 37836453 PMCID: PMC10574734 DOI: 10.3390/nu15194169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The presence of proteases and their resulting level of activity on human milk (HM) proteins may aid in the generation of indigenous peptides as part of a pre-digestion process, of which some have potential bioactivity for the infant. The present study investigated the relative abundance of indigenous peptides and their cleavage products in relation to the abundance of observed proteases and protease inhibitors. The proteomes and peptidomes in twelve HM samples, representing six donors at lactation months 1 and 3, were profiled. In the proteome, 39 proteases and 29 protease inhibitors were identified in 2/3 of the samples. Cathepsin D was found to be present in higher abundance in the proteome compared with plasmin, while peptides originating from plasmin cleavage were more abundant than peptides from cathepsin D cleavage. As both proteases are present as a system of pro- and active- forms, their activation indexes were calculated. Plasmin was more active in lactation month 3 than month 1, which correlated with the total relative abundance of the cleavage product ascribed to plasmin. By searching the identified indigenous peptides in the milk bioactive peptide database, 283 peptides were ascribed to 10 groups of bioactivities. Antimicrobial peptides were significantly more abundant in month 1 than month 3; this group comprised 103 peptides, originating from the β-CN C-terminal region.
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Affiliation(s)
- Martin Nørmark Thesbjerg
- Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Aarhus, Denmark; (M.N.T.); (N.A.P.)
- Sino-Danish College (SDC), University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Søren Drud-Heydary Nielsen
- Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Aarhus, Denmark; (M.N.T.); (N.A.P.)
| | - Ulrik Kræmer Sundekilde
- Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Aarhus, Denmark; (M.N.T.); (N.A.P.)
| | - Nina Aagaard Poulsen
- Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Aarhus, Denmark; (M.N.T.); (N.A.P.)
| | - Lotte Bach Larsen
- Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Aarhus, Denmark; (M.N.T.); (N.A.P.)
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Ning J, Li M, Chen W, Yang M, Chen J, Luo X, Yue X. Characterization and biological function analysis of endogenous peptides derived from donkey colostrum proteins. Food Funct 2023; 14:8261-8275. [PMID: 37602399 DOI: 10.1039/d3fo01703f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Donkey colostrum, due to its abundance of active ingredients, including lysozyme, proteins, and peptides, is essential for the growth and immune defence of newborns. However, research on endogenous peptides in donkey colostrum is inadequate. This study analysed the profiles of endogenous peptides, their potential bioactivity, and the enzymes that generated these peptides using two different strategies. A total of 6202 endogenous peptides were characterised through a database search, while an additional 2997 peptides were identified de novo. Among the 1142 proteins identified, trypsin and plasmin demonstrated the highest bioactivities. Furthermore, a bioinformatics-based screening identified antioxidant peptides, angiotensin I-converting enzyme inhibitory peptides, and dipeptidyl peptidase IV inhibitory peptides as the three most active peptides. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted. These findings enhance our knowledge of endogenous peptides in donkey colostrum and provide crucial information regarding these peptides as nutritional factors for the future development of functional foods derived from donkey sources.
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Affiliation(s)
- Jianting Ning
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China.
| | - Mohan Li
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China.
| | - Weiyan Chen
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China.
| | - Mei Yang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China.
| | - Jiali Chen
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China.
| | - Xue Luo
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China.
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China.
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The Impact of Low-Temperature Inactivation of Protease AprX from Pseudomonas on Its Proteolytic Capacity and Specificity: A Peptidomic Study. DAIRY 2023. [DOI: 10.3390/dairy4010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The destabilization of UHT milk during its shelf life can be promoted by the residual proteolytic activity attributed to the protease AprX from Pseudomonas. To better understand the hydrolysis patterns of AprX, and to evaluate the feasibility of using low-temperature inactivation (LTI) for AprX, the release of peptides through AprX activity on milk proteins was examined using an LC-MS/MS-based peptidomic analysis. Milk samples were either directly incubated to be hydrolyzed by AprX, or preheated under LTI conditions (60 °C for 15 min) and then incubated. Peptides and parent proteins (the proteins from which the peptides originated) were identified and quantified. The peptides were mapped and the cleavage frequency of amino acids in the P1/P1′ positions was analyzed, after which the influence of LTI and the potential bitterness of the formed peptides were determined. Our results showed that a total of 2488 peptides were identified from 48 parent proteins, with the most abundant peptides originating from κ-casein and β-casein. AprX may also non-specifically hydrolyze other proteins in milk. Except for decreasing the bitterness potential in skim UHT milk, LTI did not significantly reduce the AprX-induced hydrolysis of milk proteins. Therefore, the inactivation of AprX by LTI may not be feasible in UHT milk production.
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Goat milk-derived short chain peptides: Peptide LPYV as species-specific characteristic and their versatility bioactivities by MOF@Fe 3O 4@GO mesoporous magnetic-based peptidomics. Food Res Int 2023; 164:112442. [PMID: 36738007 DOI: 10.1016/j.foodres.2022.112442] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/25/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023]
Abstract
Goat milk as an ideal substitute for human milk has not been sufficiently explored. An in-situ synthesized MOF@Fe3O4@GO was demonstrated as a magnetic mesoporous adsorbent for efficiently enriching short chain peptides (SCPs) in milk compared with the routine solid phase extraction approach with graphite carbon black or C18 as the packing material in terms of the number of enriched SCPs and data stability. A total of 61 and 126 SCPs were identified and quantified in bovine milk (0.09-89.34 μg L-1) and goat milk (10.5-1267.06 μg L-1), respectively, and peptide LPYV can be used as a potential marker for adulteration of goat milk. Relative high expression of chymotrypsin and pepsin by EnzymePredictor analysis could partially elaborate the reason of the abundance of SCPs in goat milk. Compared with bovine milk, further bioinformatics analysis indicated that goat milk could own higher nutritional value because of relative higher concentrations (>1 mg/L) of SCPs (LLV, FL, LVYP) with confirmed bioactivities including angiotensin-converting enzyme (ACE) inhibitor, antioxidant, dipeptidylpeptidase (DPP) III and DPP IV inhibitor, etc. Overall, this study opened a novel avenue for understanding versatility benefit of dairy products from a perspective of SCPs by using a developed MOF@Fe3O4@GO mesoporous magnetic-based peptidomics.
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Shuli Z, Linlin L, Li G, Yinghu Z, Nan S, Haibin W, Hongyu X. Bioinformatics and Computer Simulation approaches to the discovery and analysis of Bioactive Peptides. Curr Pharm Biotechnol 2022; 23:1541-1555. [PMID: 34994325 DOI: 10.2174/1389201023666220106161016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/16/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022]
Abstract
The traditional process of separating and purifying bioactive peptides is laborious and time-consuming. Using a traditional process to identify is difficult, and there is a lack of fast and accurate activity evaluation methods. How to extract bioactive peptides quickly and efficiently is still the focus of bioactive peptides research. In order to improve the present situation of the research, bioinformatics techniques and peptidome methods are widely used in this field. At the same time, bioactive peptides have their own specific pharmacokinetic characteristics, so computer simulation methods have incomparable advantages in studying the pharmacokinetics and pharmacokinetic-pharmacodynamic correlation models of bioactive peptides. The purpose of this review is to summarize the combined applications of bioinformatics and computer simulation methods in the study of bioactive peptides, with focuses on the role of bioinformatics in simulating the selection of enzymatic hydrolysis and precursor proteins, activity prediction, molecular docking, physicochemical properties, and molecular dynamics. Our review shows that new bioactive peptide molecular sequences with high activity can be obtained by computer-aided design. The significance of the pharmacokinetic-pharmacodynamic correlation model in the study of bioactive peptides is emphasized. Finally, some problems and future development potential of bioactive peptides binding new technologies are prospected.
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Affiliation(s)
- Zhang Shuli
- School of Chemical Engineering and Technology, North University of China, Taiyuan, Shanxi, 030051, China
| | - Liu Linlin
- School of Chemical Engineering and Technology, North University of China, Taiyuan, Shanxi, 030051, China
| | - Gao Li
- School of Chemical Engineering and Technology, North University of China, Taiyuan, Shanxi, 030051, China
| | - Zhao Yinghu
- School of Environment and Safety Engineering, North University of China, Taiyuan, Shanxi, 030051, China
| | - Shi Nan
- School of Chemical Engineering and Technology, North University of China, Taiyuan, Shanxi, 030051, China
| | - Wang Haibin
- School of Chemical Engineering and Technology, North University of China, Taiyuan, Shanxi, 030051, China
| | - Xu Hongyu
- School of Chemical Engineering and Technology, North University of China, Taiyuan, Shanxi, 030051, China
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Vahedifar A, Wu J. Self-assembling peptides: Structure, function, in silico prediction and applications. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2021.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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12
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Petit N, Dyer JM, Clerens S, Gerrard JA, Domigan LJ. Oral delivery of self-assembling bioactive peptides to target gastrointestinal tract disease. Food Funct 2021; 11:9468-9488. [PMID: 33155590 DOI: 10.1039/d0fo01801e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Peptides are known for their diverse bioactivities including antioxidant, antimicrobial, and anticancer activity, all three of which are potentially useful in treating colon-associated diseases. Beside their capability to stimulate positive health effects once released in the body, peptides are able to form useful nanostructures such as hydrogels. Combining peptide bioactivity and peptide gel-forming potentials can create interesting systems that can be used for oral delivery. This combination, acting as a two-in-one system, has the potential to avoid the need for delicate entrapment of a drug or natural bioactive compound. We here review the context and research progress, to date, in this area.
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Affiliation(s)
- Noémie Petit
- Riddet Institute, Massey University, PB 11 222, Palmerston North 4442, New Zealand
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Leite JAS, Montoya CA, Loveday SM, Maes E, Mullaney JA, McNabb WC, Roy NC. Heat-Treatments Affect Protease Activities and Peptide Profiles of Ruminants' Milk. Front Nutr 2021; 8:626475. [PMID: 33777990 PMCID: PMC7987661 DOI: 10.3389/fnut.2021.626475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/08/2021] [Indexed: 01/30/2023] Open
Abstract
Proteases present in milk are heat-sensitive, and their activities increase or decrease depending on the intensity of the thermal treatment applied. The thermal effects on the protease activity are well-known for bovine milk but poorly understood for ovine and caprine milk. This study aimed to determine the non-specific and specific protease activities in casein and whey fractions isolated from raw bovine, ovine, and caprine milk collected in early lactation, and to determine the effects of low-temperature, long-time (63°C for 30 min) and high-temperature, short-time (85°C for 5 min) treatments on protease activities within each milk fraction. The non-specific protease activities in raw and heat-treated milk samples were determined using the substrate azocasein. Plasmin (the main protease in milk) and plasminogen-derived activities were determined using the chromogenic substrate S-2251 (D-Val-Leu-Lys-pNA dihydrochloride). Peptides were characterized using high-resolution liquid chromatography coupled with tandem mass spectrometry. The activity of all native proteases, shown as non-specific proteases, was similar between raw bovine and caprine milk samples, but lower (P < 0.05) than raw ovine milk in the whey fraction. There was no difference (P > 0.05) between the non-specific protease activity of the casein fraction of raw bovine and caprine milk samples; both had higher activity than ovine milk. After 63°C/30 min, the non-specific protease activity decreased (44%; P > 0.05) for the bovine casein fraction only. In contrast, the protease activity of the milk heated at 85°C/5 min changed depending on the species and fraction. For instance, the activity decreased by 49% for ovine whey fraction, but it increased by 68% for ovine casein fraction. Plasmin and plasminogen were in general inactivated (P > 0.05) when all milk fractions were heated at 85°C/5 min. Most of the peptides present in heat-treated milk were derived from β-casein and αS1-casein, and they matched the hydrolysis profile of cathepsin D and plasmin. Identified peptides in ruminant milk samples had purported immunomodulatory and inhibitory functions. These findings indicate that the non-specific protease activity in whey and casein fractions differed between ruminant milk species, and specific thermal treatments could be used to retain better protease activity for all ruminant milk species.
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Affiliation(s)
| | - Carlos A. Montoya
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Smart Foods Innovation Centre of Excellence, AgResearch Limited, Palmerston North, New Zealand
| | - Simon M. Loveday
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Smart Foods Innovation Centre of Excellence, AgResearch Limited, Palmerston North, New Zealand
| | - Evelyne Maes
- Beyond Foods Innovation Centre of Excellence, AgResearch Limited, Lincoln, New Zealand
| | - Jane A. Mullaney
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Smart Foods Innovation Centre of Excellence, AgResearch Limited, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Warren C. McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nicole C. Roy
- Riddet Institute, Massey University, Palmerston North, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- Department of Nutrition, University of Otago, Dunedin, New Zealand
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14
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Barati M, Javanmardi F, Mousavi Jazayeri SMH, Jabbari M, Rahmani J, Barati F, Nickho H, Davoodi SH, Roshanravan N, Mousavi Khaneghah A. Techniques, perspectives, and challenges of bioactive peptide generation: A comprehensive systematic review. Compr Rev Food Sci Food Saf 2020; 19:1488-1520. [PMID: 33337080 DOI: 10.1111/1541-4337.12578] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 04/03/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022]
Abstract
Due to the digestible refractory and absorbable structures of bioactive peptides (BPs), they could induce notable biological impacts on the living organism. In this regard, the current study was devoted to providing an overview regarding the available methods for BPs generation by the aid of a systematic review conducted on the published articles up to April 2019. In this context, the PubMed and Scopus databases were screened to retrieve the related publications. According to the results, although the characterization of BPs mainly has been performed using enzymatic and microbial in-vitro methods, they cannot be considered as suitable techniques for further stimulation of digestion in the gastrointestinal tract. Therefore, new approaches for both in-vivo and in-silico methods for BPs identification should be developed to overcome the obstacles that belonged to the current methods. The purpose of this review was to compile the recent analytical methods applied for studying various aspects of food-derived biopeptides, and emphasizing generation at in vitro, in vivo, and in silico.
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Affiliation(s)
- Meisam Barati
- Student Research Committee, Department of Cellular and Molecular Nutrition, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fardin Javanmardi
- Department of Food Science and Technology, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Masoumeh Jabbari
- Department of Community Nutrition, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamal Rahmani
- Department of Community Nutrition, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzaneh Barati
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Hamid Nickho
- Immunology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sayed Hossein Davoodi
- Department of Clinical Nutrition and Dietetic, National Institute and Faculty of Nutrition and Food Technology; Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Neda Roshanravan
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amin Mousavi Khaneghah
- Department of Food Science, Faculty of Food Engineering, University of Campinas (UNICAMP), São Paulo, Brazil
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15
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Comparative Peptidomic and Metatranscriptomic Analyses Reveal Improved Gamma-Amino Butyric Acid Production Machinery in Levilactobacillus brevis Strain NPS-QW 145 Cocultured with Streptococcus thermophilus Strain ASCC1275 during Milk Fermentation. Appl Environ Microbiol 2020; 87:AEM.01985-20. [PMID: 33067198 DOI: 10.1128/aem.01985-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022] Open
Abstract
The high-gamma-amino butyric acid (GABA)-producing bacterium Levilactobacillus brevis strain NPS-QW 145, along with Streptococcus thermophilus (one of the two starter bacteria used to make yogurt for its proteolytic activity), enhances GABA production in milk. However, a mechanistic understanding of how Levilactobacillus brevis cooperates with S. thermophilus to stimulate GABA production has been lacking. Comparative peptidomic and metatranscriptomic analyses were carried out to unravel the casein and lactose utilization patterns during milk fermentation with the coculture. We found that particular peptides hydrolyzed by S. thermophilus ASCC1275 were transported and biodegraded with peptidase in Lb. brevis 145 to meet the growth needs of the latter. In addition, amino acid synthesis and metabolism in Lb. brevis 145 were activated to further support its growth. Glucose, as a result of lactose hydrolysis by S. thermophilus 1275, but not available lactose in milk, was metabolized as the main carbon source by Lb. brevis 145 for ATP production. In the stationary phase, under acidic conditions due to the accumulation of lactic acid produced by S. thermophilus 1275, the expression of genes involved in pyridoxal phosphate (coenzyme of glutamic acid decarboxylase) metabolism and glutamic acid decarboxylase (Gad) in Lb. brevis 145 was induced for GABA production.SIGNIFICANCE A huge market for GABA-rich milk as a dietary therapy for the management of hypertension is anticipated. The novelty of this work lies in applying peptide profiles supported by metatranscriptomics to elucidate (i) the pattern of casein hydrolysis by S. thermophilus 1275, (ii) the supply of peptides and glucose by S. thermophilus 1275 to Lb. brevis 145, (iii) the transportation of peptides in Lb. brevis and the degradation of peptides by this organism, which was reported to be nonproteolytic, and (iv) GABA production by Lb. brevis 145 under acidic conditions. Based on the widely reported contribution of lactic acid bacteria (LAB) and GABA to human health, the elucidation of interactions between the two groups of bacterial communities in the production of GABA-rich milk is important for promoting the development of functional dairy food and may provide new insight into the development of industrial GABA production.
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16
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Digestion of micellar casein in duodenum cannulated pigs. Correlation between in vitro simulated gastric digestion and in vivo data. Food Chem 2020; 343:128424. [PMID: 33127229 DOI: 10.1016/j.foodchem.2020.128424] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 11/21/2022]
Abstract
Correlation and validation of the results of simulated gastrointestinal digestion of food compounds towards in vivo data is essential. The objective of this work was to monitor the digestion of milk micellar casein in the porcine upper intestinal tract and to match the outcome with the gastric in vitro digestion following the Infogest harmonized protocol. In pig duodenum, small amounts of intact caseins were present in all samples, while caseins were observed up to 60 min of gastric in vitro digestion. The peptide profile generated after in vitro and in vivo digestion showed clear similarities with specific overrepresented regions rich in proline and other hydrophobic residues. The statistical comparison of the in vivo and in vitro peptidome resulted in satisfactory correlation coefficients, up to 0.8. Therefore, the in vitro protocol used was a robust and simple model that provides a similar peptide profile than that found in porcine duodenum.
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17
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Insights into the evolution of myosin light chain isoforms and its effect on sensory defects of dry-cured ham. Food Chem 2020; 315:126318. [PMID: 32035317 DOI: 10.1016/j.foodchem.2020.126318] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 01/15/2023]
Abstract
To better understand the contribution of myosin light chain (MLC) isoforms to sensory defects in Jinhua ham, dipeptidyl peptidase (DPP) activities, peptide fragments, cleavage sites and the potential of DPP to develop sensory defects of dry-cured ham were evaluated and discussed in normal and defective hams. Higher residual activities of DPP I were found in defective ham compared with normal ham; approximate 3-fold peptide fragments were identified in defective ham than in normal ham. These regions of positions 11-35 and 116-141 in MLC 1, 13-53 and 139-156 in MLC 2, and 18-50 in MLC 3 contributed to the intense generation of peptide fragments in defective ham. PLS-DA further revealed DPP I showing intense response to degrade peptides. Cleavage sites including Glu-128, Tyr-132 and Glu-133 were responsible for the intense release of dipeptides in defective ham. These cleavages could play key role in discriminating taste attributes between defective and normal hams.
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18
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Peng J, Zhang H, Niu H, Wu R. Peptidomic analyses: The progress in enrichment and identification of endogenous peptides. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115835] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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19
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Tang H, Zhang J, Shi K, Aihara H, Du G. Insight into subtilisin E-S7 cleavage pattern based on crystal structure and hydrolysates peptide analysis. Biochem Biophys Res Commun 2019; 512:623-628. [PMID: 30914195 PMCID: PMC6541920 DOI: 10.1016/j.bbrc.2019.03.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 03/11/2019] [Indexed: 01/07/2023]
Abstract
The X-ray crystallographic structure of the mature form of subtilisin E-S7 (SES7) at 1.90 Å resolution is reported here. Structural comparisons between the previously reported propeptide-subtilisin E complex (1SCJ) and our mature form subtilisin E-S7 (6O44) provide insight into active site adjustments involved in catalysis and specificity. To further investigate the protease substrate selectivity mechanism, we used SES7 to hydrolyze skim milk and analyzed the hydrolysates by LC-MS for peptide identification. The cleavage pattern suggests a high preference for proline at substrate P2 position. The results based on the peptide analysis are consistent with our structural observations, which is instrumental in future protein engineering by rational design. Furthermore, the ACE-inhibitor and NLN-inhibitor activity of the hydrolysates were determined to assess the utility of SES7 for further industrial applications; IC50-ACE = 67 ± 0.92 μg/mL and IC50-NLN = 263 ± 13 μg/mL.
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Affiliation(s)
- Heng Tang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, Chi
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, Chi
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA.,Corresponding authors: Hideki Aihara, ., Guocheng Du,
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, Chi,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China,Corresponding authors: Hideki Aihara, ., Guocheng Du,
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20
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Vitorino R. Digging Deep into Peptidomics Applied to Body Fluids. Proteomics 2019; 18. [PMID: 29251826 DOI: 10.1002/pmic.201700401] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/06/2017] [Indexed: 12/27/2022]
Abstract
Peptidomics techniques have allowed the identification of thousands of peptides that are derived from proteins in body fluids, despite the considerable challenges behind sample handling, MS-based identification, data analysis, and integration with bioinformatics tools. Body fluids' naturally occurring peptides are known to perform a variety of local and systemic functions; however, its knowledge is limited. Even so, the biological meaning that can be retrieved from peptidomics applied to the identification of disease markers and to the development of therapies using peptides has driven the progresses made in this field. In this review, a comparative analysis of body fluids' peptidome data retrieved from databases and from scientific papers is performed to identify the biological processes modulated by naturally occurring peptides. This integrative analysis highlights several interesting facts, such as the small overlap between blood-derived serum and plasma, which illustrates the impact of sample handling on these fluids peptidome. Urine is the body fluid with more naturally occurring peptides identified so far, most of which are derived from collagens. In saliva, the majority of peptides are originated from extracellular matrix proteins. Cerebrospinal fluid presents a high number of peptides derived from distinct proteins, mostly involved in the regulation of nervous system homeostasis. The lowest number of endogenous peptides was found in tears, most of which present antimicrobial activity. Collectively, data analysis highlights a peptidome signature for each body fluid, which comprehension will certainly help to improve disease management.
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Affiliation(s)
- Rui Vitorino
- iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Universidade do Porto, Porto, Portugal
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21
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Enjapoori AK, Kukuljan S, Dwyer KM, Sharp JA. In vivo endogenous proteolysis yielding beta-casein derived bioactive beta-casomorphin peptides in human breast milk for infant nutrition. Nutrition 2019; 57:259-267. [DOI: 10.1016/j.nut.2018.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/15/2018] [Accepted: 05/29/2018] [Indexed: 10/28/2022]
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22
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Deglaire A, Oliveira SD, Jardin J, Briard-Bion V, Kroell F, Emily M, Ménard O, Bourlieu C, Dupont D. Impact of human milk pasteurization on the kinetics of peptide release during in vitro dynamic digestion at the preterm newborn stage. Food Chem 2018; 281:294-303. [PMID: 30658760 DOI: 10.1016/j.foodchem.2018.12.086] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 01/25/2023]
Abstract
Holder pasteurization (62.5 °C, 30 min) of human milk denatures beneficial proteins. The present paper aimed to assess whether this can affect the kinetics of peptide release during digestion at the preterm stage. Raw (RHM) or pasteurized (PHM) human milk were digested in triplicates using an in vitro dynamic system. Mass spectrometry and multivariate statistics were conducted. Pre-proteolysis occurred mostly on β-casein, for which cumulative peptide abundance was significantly greater in PHM over 28% of the hydrolysed sequence. Eight clusters resumed the kinetics of peptide release during digestion, which differed on seven clusters (69% of the 1134 peptides). Clusters associated to the heat-denaturated proteins, lactoferrin and bile salt-stimulated lipase, presented different kinetics of release during digestion, unlike that for β-casein. Some bioactive peptides from β-casein presented significant different abundances between PHM and RHM before digestion (1-18, 185-211) or in during intestinal digestion (154-160, 161-166). Further physiological consequences should be investigated.
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Affiliation(s)
| | | | | | | | - Florian Kroell
- STLO, Agrocampus Ouest, INRA, 35042 Rennes, France; IRMAR, Agrocampus Ouest, CNRS, 35042 Rennes, France
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23
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Maestri E, Pavlicevic M, Montorsi M, Marmiroli N. Meta-Analysis for Correlating Structure of Bioactive Peptides in Foods of Animal Origin with Regard to Effect and Stability. Compr Rev Food Sci Food Saf 2018; 18:3-30. [PMID: 33337011 DOI: 10.1111/1541-4337.12402] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 09/28/2018] [Accepted: 09/29/2018] [Indexed: 01/09/2023]
Abstract
Amino acid (AA) sequences of 807 bioactive peptides from foods of animal origin were examined in order to correlate peptide structure with activity (antihypertensive, antioxidative, immunomodulatory, antimicrobial, hypolipidemic, antithrombotic, and opioid) and stability in vivo. Food sources, such as milk, meat, eggs, and marine products, show different frequencies of bioactive peptides exhibiting specific effects. There is a correlation of peptide structure and effect, depending on type and position of AA. Opioid peptides contain a high percentage of aromatic AA residues, while antimicrobial peptides show an excess of positively charged AAs. AA residue position is significant, with those in the first and penultimate positions having the biggest effects on peptide activity. Peptides that have activity in vivo contain a high percentage (67%) of proline residues, but the positions of proline in the sequence depend on the length of the peptide. We also discuss the influence of processing on activity of these peptides, as well as methods for predicting release from the source protein and activity of peptides.
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Affiliation(s)
- Elena Maestri
- Dept. of Chemistry, Life Sciences and Environmental Sustainability, Univ. of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy.,Interdepartmental Centre for Food Safety, Technologies and Innovation for Agri-food (SITEIA.PARMA), Univ. of Parma, Parco Area delle Scienze, 43124, Parma, Italy
| | - Milica Pavlicevic
- Inst. for Food Technology and Biochemistry, Faculty of Agriculture, Univ. of Belgrade, Belgrade, Serbia
| | - Michela Montorsi
- Dept. of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open Univ., Via F. Daverio 7, 20122, Milan, Italy.,Consorzio Italbiotec, Via Fantoli, 16/15, 20138, Milano, Italy.,Inst. of Bioimaging and Molecular Physiology, National Council of Research (CNR), Via Fratelli Cervi 93, 20090, Segrate, Italy
| | - Nelson Marmiroli
- Dept. of Chemistry, Life Sciences and Environmental Sustainability, Univ. of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy.,Interdepartmental Centre for Food Safety, Technologies and Innovation for Agri-food (SITEIA.PARMA), Univ. of Parma, Parco Area delle Scienze, 43124, Parma, Italy.,Consorzio Italbiotec, Via Fantoli, 16/15, 20138, Milano, Italy
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24
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Kalmykova SD, Arapidi GP, Urban AS, Osetrova MS, Gordeeva VD, Ivanov VT, Govorun VM. In Silico Analysis of Peptide Potential Biological Functions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s106816201804009x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Tu M, Cheng S, Lu W, Du M. Advancement and prospects of bioinformatics analysis for studying bioactive peptides from food-derived protein: Sequence, structure, and functions. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.04.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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26
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Dingess KA, de Waard M, Boeren S, Vervoort J, Lambers TT, van Goudoever JB, Hettinga K. Human milk peptides differentiate between the preterm and term infant and across varying lactational stages. Food Funct 2018; 8:3769-3782. [PMID: 28959809 DOI: 10.1039/c7fo00539c] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Variations in endogenous peptide profiles, functionality, and the enzymes responsible for the formation of these peptides in human milk are understudied. Additionally, there is a lack of knowledge regarding peptides in donor human milk, which is used to feed preterm infants when mother's own milk is not (sufficiently) available. To assess this, 29 human milk samples from the Dutch Human Milk Bank were analyzed as three groups, preterm late lactation stage (LS) (n = 12), term early (n = 8) and term late LS (n = 9). Gestational age (GA) groups were defined as preterm (24-36 weeks) and term (≥37 weeks). LS was determined as days postpartum as early (16-36 days) or late (55-88 days). Peptides, analyzed by LC-MS/MS, and parent proteins (proteins from matched peptide sequences) were identified and quantified, after which peptide functionality and the enzymes responsible for protein cleavage were determined. A total of 16 different parent proteins were identified from human milk, with no differences by GA or LS. We identified 1104 endogenous peptides, of which, the majority were from the parent proteins β-casein, polymeric immunoglobulin receptor, αs1-casein, osteopontin, and κ-casein. The absolute number of peptides differed by GA and LS with 30 and 41 differing sequences respectively (p < 0.05) Odds likelihood tests determined that 32 peptides had a predicted bioactive functionality, with no significant differences between groups. Enzyme prediction analysis showed that plasmin/trypsin enzymes most likely cleaved the identified human milk peptides. These results explain some of the variation in endogenous peptides in human milk, leading to future targets that may be studied for functionality.
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Affiliation(s)
- Kelly A Dingess
- Dairy Science and Technology, Food Quality and Design Group, Wageningen University, The Netherlands.
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27
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Moreno-Montoro M, Jauregi P, Navarro-Alarcón M, Olalla-Herrera M, Giménez-Martínez R, Amigo L, Miralles B. Bioaccessible peptides released by in vitro gastrointestinal digestion of fermented goat milks. Anal Bioanal Chem 2018. [PMID: 29523944 DOI: 10.1007/s00216-018-0983-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this study, ultrafiltered goat milks fermented with the classical starter bacteria Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus salivarus subsp. thermophilus or with the classical starter plus the Lactobacillus plantarum C4 probiotic strain were analyzed using ultra-high performance liquid chromatography-quadrupole-time-of-flight tandem mass spectrometry (UPLC-Q-TOF-MS/MS) and/or high performance liquid chromatography-ion trap (HPLC-IT-MS/MS). Partial overlapping of the identified sequences with regard to fermentation culture was observed. Evaluation of the cleavage specificity suggested a lower proteolytic activity of the probiotic strain. Some of the potentially identified peptides had been previously reported as angiotensin-converting enzyme (ACE) inhibitory, antioxidant, and antibacterial and might account for the in vitro activity previously reported for these fermented milks. Simulated digestion of the products was conducted in the presence of a dialysis membrane to retrieve the bioaccessible peptide fraction. Some sequences with reported physiological activity resisted digestion but were found in the non-dialyzable fraction. However, new forms released by digestion, such as the antioxidant αs1-casein 144YFYPQL149, the antihypertensive αs2-casein 90YQKFPQY96, and the antibacterial αs2-casein 165LKKISQ170, were found in the dialyzable fraction of both fermented milks. Moreover, in the fermented milk including the probiotic strain, the k-casein dipeptidyl peptidase IV inhibitor (DPP-IV) 51INNQFLPYPY60 as well as additional ACE inhibitory or antioxidant sequences could be identified. With the aim of anticipating further biological outcomes, quantitative structure activity relationship (QSAR) analysis was applied to the bioaccessible fragments and led to potential ACE inhibitory sequences being proposed. Graphical abstract Ultrafiltered goat milks were fermented with the classical starter bacteria (St) and with St plus the L. plantarum C4 probiotic strain. Samples were analyzed using HPLC-IT-MS/MS and UPLC-Q-TOF-MS/MS. After simulated digestion and dialysis, some of the active sequences remained and new peptides with reported beneficial activities were released.
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Affiliation(s)
- Miriam Moreno-Montoro
- Department of Nutrition and Food Science, Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071, Granada, Spain
| | - Paula Jauregi
- Department of Food and Nutritional Sciences, The University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP, UK
| | - Miguel Navarro-Alarcón
- Department of Nutrition and Food Science, Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071, Granada, Spain
| | - Manuel Olalla-Herrera
- Department of Nutrition and Food Science, Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071, Granada, Spain
| | - Rafael Giménez-Martínez
- Department of Nutrition and Food Science, Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071, Granada, Spain
| | - Lourdes Amigo
- Department of Bioactivity and Food Analysis, Institute of Food Science Research (CIAL, CSIC-UAM), c/Nicolas Cabrera 9, 28049, Madrid, Spain
| | - Beatriz Miralles
- Department of Bioactivity and Food Analysis, Institute of Food Science Research (CIAL, CSIC-UAM), c/Nicolas Cabrera 9, 28049, Madrid, Spain.
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28
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Saliva as a source of new phosphopeptide biomarkers: Development of a comprehensive analytical method based on shotgun peptidomics. Talanta 2018; 183:245-249. [PMID: 29567172 DOI: 10.1016/j.talanta.2018.02.085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 12/15/2022]
Abstract
The paper describes the development of an enrichment method for the analysis of the endogenous phosphopeptides in saliva. The method was based on magnetic solid phase extraction by a magnetic graphitized carbon black-TiO2 composite material and was developed considering different saliva pre-treatments, namely C18 solid phase extraction for purification, direct dilution in loading buffer or acetonitrile precipitation. The method was based on a shotgun proteomics workflow and the enriched peptide mixture was analysed by nanoHPLC and high resolution tandem mass spectrometry. Acetonitrile precipitation provided the best results, with up to 165 endogenous phosphopeptides identified in saliva samples from healthy individuals. The physico-chemical features of the identified endogenous phosphopeptides indicated that such peptides were large, hydrophilic and basic.
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29
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Dallas D, Nielsen SD. Milk Peptidomics to Identify Functional Peptides and for Quality Control of Dairy Products. Methods Mol Biol 2018; 1719:223-240. [PMID: 29476515 DOI: 10.1007/978-1-4939-7537-2_15] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human milk and dairy products are important parts of human nutrition. In addition to supplying nutrients, milk proteins contain fragments-peptides-with important biological functions that are released during processing or digestion. Besides their potential functional relevance, peptides released during processing can be used as markers of ripening stage or product deterioration. Hence, identification and quantification of peptides in milk can be used to assay potential health benefits or product quality. This chapter describes how to extract, identify, and analyze peptides within breast milk, dairy products, and dairy digestive samples. We describe how to analyze extracted peptides with liquid chromatography-mass spectrometry, to use software to identify peptides based on database searching, and to extract peak areas for relative quantification of each peptide. We describe methods for data analysis, including predicting which enzymes are responsible for protein cleavage, identifying the site specificity of protein breakdown, mapping identified peptides to known bioactive peptides, and applying models to predict novel functional peptides.
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Affiliation(s)
- David Dallas
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA.
| | - Søren Drud Nielsen
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
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30
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Nielsen SD, Beverly RL, Dallas DC. Peptides Released from Foremilk and Hindmilk Proteins by Breast Milk Proteases Are Highly Similar. Front Nutr 2017; 4:54. [PMID: 29164128 PMCID: PMC5673630 DOI: 10.3389/fnut.2017.00054] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/19/2017] [Indexed: 11/13/2022] Open
Abstract
Human milk contains active proteases that initiate hydrolysis of milk proteins within the mammary gland. Milk expressed at the beginning of feeding is known as foremilk and that at the end of feeding is known as hindmilk. As hindmilk contains higher fat, vitamins A and E, and higher calories than foremilk, feeding only hindmilk initially and reserving foremilk for later are practiced in some neonatal intensive care units. This study investigated the difference in peptide profiles, predicted milk protease activities, and bioactive peptides between foremilk and hindmilk. Bioactive peptides are short fragments of proteins that influence biological processes. Four mothers pumped 10 mL of their foremilk and 10 mL of their hindmilk into iced containers prepared with antiproteases and the samples were immediately frozen. The peptide profile of each sample was analyzed by liquid chromatography nano-electrospray ionization Orbitrap Fusion tandem mass spectrometry. Peptide abundance (sum of ion intensities) and count (number of unique peptide sequences) in each milk sample were determined from this analysis. The specific enzymes that participated in peptide release were predicted based on the amino acids positioned at each cleavage site. Peptide bioactivity was predicted based on homology to a known functional peptide database and two bioactivity prediction algorithms. Hindmilk contained a higher count of peptides than foremilk. The higher number of unique peptide sequences in hindmilk was related to hydrolysis of β-casein, osteopontin, αs1-casein and mucin-1 via plasmin and elastase cleavage, and possible aminopeptidase and carboxypeptidase activities. Though hindmilk contained a greater number of peptides than foremilk, the overall peptide abundance did not differ and most of the total peptide abundance derived from peptide sequences that were present in both milk types. The presence of higher numbers of predicted bioactive peptides in the hindmilk could indicate that the practice of providing hindmilk rather than foremilk to premature infants could positively impact health outcomes; however, as there are few differences in overall peptide abundance, the overall effect is likely limited.
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Affiliation(s)
- Søren D Nielsen
- Nutrition Program, School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, United States
| | - Robert L Beverly
- Nutrition Program, School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, United States
| | - David C Dallas
- Nutrition Program, School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, United States
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31
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Challenges in the quantitation of naturally generated bioactive peptides in processed meats. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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32
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Bounouala FZ, Roudj S, Karam NE, Recio I, Miralles B. Casein Hydrolysates by Lactobacillus brevis and Lactococcus lactis Proteases: Peptide Profile Discriminates Strain-Dependent Enzyme Specificity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:9324-9332. [PMID: 28965394 DOI: 10.1021/acs.jafc.7b03203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Casein from ovine and bovine milk were hydrolyzed with two extracellular protease preparations from Lactobacillus brevis and Lactococcus lactis. The hydrolysates were analyzed by HPLC-MS/MS for peptide identification. A strain-dependent peptide profile could be observed, regardless of the casein origin, and the specificity of these two proteases could be computationally ascribed. The cleavage pattern yielding phenylalanine, leucine, or tyrosine at C-terminal appeared both at L. lactis and Lb. brevis hydrolysates. However, the cleavage C-terminal to lysine was favored with Lb. brevis protease. The hydrolysates showed ACE-inhibitory activity with IC50 in the 16-70 μg/mL range. Ovine casein hydrolysates yielded greater ACE-inhibitory activity. Previously described antihypertensive and opioid peptides were found in these ovine and bovine casein hydrolysates and prediction of the antihypertensive activity of the sequences based on quantitative structure and activity relationship (QSAR) was performed. This approach might represent a useful classification tool regarding health-related properties prior to further purification.
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Affiliation(s)
- Fatima Zohra Bounouala
- Instituto de Investigación en Ciencias de la Alimentación, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid (CIAL, CSIC-UAM) , Nicolás Cabrera 9, 28049 Madrid, Spain
- Laboratoire de Biologie des Microorganismes et Biotechnologie (LBMB). Université d'Oran 1 Ahmed Ben Bella , BP 1524 Oran El Mnaouer, 31000, Oran, Algérie
| | - Salima Roudj
- Laboratoire de Biologie des Microorganismes et Biotechnologie (LBMB). Université d'Oran 1 Ahmed Ben Bella , BP 1524 Oran El Mnaouer, 31000, Oran, Algérie
| | - Nour-Eddine Karam
- Laboratoire de Biologie des Microorganismes et Biotechnologie (LBMB). Université d'Oran 1 Ahmed Ben Bella , BP 1524 Oran El Mnaouer, 31000, Oran, Algérie
| | - Isidra Recio
- Instituto de Investigación en Ciencias de la Alimentación, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid (CIAL, CSIC-UAM) , Nicolás Cabrera 9, 28049 Madrid, Spain
| | - Beatriz Miralles
- Instituto de Investigación en Ciencias de la Alimentación, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid (CIAL, CSIC-UAM) , Nicolás Cabrera 9, 28049 Madrid, Spain
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Greening DW, Kapp EA, Simpson RJ. The Peptidome Comes of Age: Mass Spectrometry-Based Characterization of the Circulating Cancer Peptidome. Enzymes 2017; 42:27-64. [PMID: 29054270 DOI: 10.1016/bs.enz.2017.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Peptides play a seminal role in most physiological processes acting as neurotransmitters, hormones, antibiotics, and immune regulation. In the context of tumor biology, it is hypothesized that endogenous peptides, hormones, cytokines, growth factors, and aberrant degradation of select protein networks (e.g., enzymatic activities, protein shedding, and extracellular matrix remodeling) are fundamental in mediating cancer progression. Analysis of peptides in biological fluids by mass spectrometry holds promise of providing sensitive and specific diagnostic and prognostic information for cancer and other diseases. The identification of circulating peptides in the context of disease constitutes a hitherto source of new clinical biomarkers. The field of peptidomics can be defined as the identification and comprehensive analysis of physiological and pathological peptides. Like proteomics, peptidomics has been advanced by the development of new separation strategies, analytical detection methods such as mass spectrometry, and bioinformatic technologies. Unlike proteomics, peptidomics is targeted toward identifying endogenous protein and peptide fragments, defining proteolytic enzyme substrate specificity, as well as protease cleavage recognition (degradome). Peptidomics employs "top-down proteomics" strategies where mass spectrometry is applied at the proteoform level to analyze intact proteins and large endogenous peptide fragments. With recent advances in prefractionation workflows for separating peptides, mass spectrometry instrumentation, and informatics, peptidomics is an important field that promises to impact on translational medicine. This review covers the current advances in peptidomics, including top-down and imaging mass spectrometry, comprehensive quantitative peptidome analyses (developments in reproducibility and coverage), peptide prefractionation and enrichment workflows, peptidomic data analyses, and informatic tools. The application of peptidomics in cancer biomarker discovery will be discussed.
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Affiliation(s)
- David W Greening
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
| | - Eugene A Kapp
- Systems Biology & Personalised Medicine Division, Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Florey Institute of Neuroscience, Parkville, Victoria, Australia; University of Melbourne, Parkville, Victoria, Australia
| | - Richard J Simpson
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
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Sanchón J, Fernández-Tomé S, Miralles B, Hernández-Ledesma B, Tomé D, Gaudichon C, Recio I. Protein degradation and peptide release from milk proteins in human jejunum. Comparison with in vitro gastrointestinal simulation. Food Chem 2017; 239:486-494. [PMID: 28873595 DOI: 10.1016/j.foodchem.2017.06.134] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/20/2017] [Accepted: 06/23/2017] [Indexed: 11/16/2022]
Abstract
Human jejunal digests after oral ingestion of casein and whey protein were collected by a nasogastric tube and protein degradation and peptide release was compared with that found in the digests of the same substrates using a standardised protocol. No intact casein was detected in the jejunal nor in the in vitro samples taken during the intestinal phase, while β-lactoglobulin was found in one hour-jejunal samples in agreement with the in vitro digestion. In vivo and in vitro digests showed comparable peptide profiles and high number of common sequences. A selective precipitation step was used to strengthen the identification of phosphorylated peptides. Most of the sequences found in jejunum, some of them not previously described, were also identified in the simulated digests. Common resistant regions to digestion were identified, revealing that the in vitro protocol constitutes a good approximation to the physiological gastrointestinal digestion of milk proteins.
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Affiliation(s)
- J Sanchón
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM, CEI UAM+CSIC), Nicolás Cabrera, 9, 28049 Madrid, Spain
| | - S Fernández-Tomé
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM, CEI UAM+CSIC), Nicolás Cabrera, 9, 28049 Madrid, Spain
| | - B Miralles
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM, CEI UAM+CSIC), Nicolás Cabrera, 9, 28049 Madrid, Spain
| | - B Hernández-Ledesma
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM, CEI UAM+CSIC), Nicolás Cabrera, 9, 28049 Madrid, Spain
| | - D Tomé
- AgroParisTech_UMR0914 Physiologie de la Nutrition et du Comportement Alimentaire, 16 rue Claude Bernard, 75005 Paris, France
| | - C Gaudichon
- AgroParisTech_UMR0914 Physiologie de la Nutrition et du Comportement Alimentaire, 16 rue Claude Bernard, 75005 Paris, France
| | - I Recio
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM, CEI UAM+CSIC), Nicolás Cabrera, 9, 28049 Madrid, Spain.
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Manguy J, Jehl P, Dillon ET, Davey NE, Shields DC, Holton TA. Peptigram: A Web-Based Application for Peptidomics Data Visualization. J Proteome Res 2016; 16:712-719. [PMID: 27997202 DOI: 10.1021/acs.jproteome.6b00751] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tandem mass spectrometry (MS/MS) techniques, developed for protein identification, are increasingly being applied in the field of peptidomics. Using this approach, the set of protein fragments observed in a sample of interest can be determined to gain insights into important biological processes such as signaling and other bioactivities. As the peptidomics era progresses, there is a need for robust and convenient methods to inspect and analyze MS/MS derived data. Here, we present Peptigram, a novel tool dedicated to the visualization and comparison of peptides detected by MS/MS. The principal advantage of Peptigram is that it provides visualizations at both the protein and peptide level, allowing users to simultaneously visualize the peptide distributions of one or more samples of interest, mapped to their parent proteins. In this way rapid comparisons between samples can be made in terms of their peptide coverage and abundance. Moreover, Peptigram integrates and displays key sequence features from external databases and links with peptide analysis tools to offer the user a comprehensive peptide discovery resource. Here, we illustrate the use of Peptigram on a data set of milk hydrolysates. For convenience, Peptigram is implemented as a web application, and is freely available for academic use at http://bioware.ucd.ie/peptigram .
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Affiliation(s)
- Jean Manguy
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
| | - Peter Jehl
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
| | - Eugène T Dillon
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
| | - Norman E Davey
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
| | - Denis C Shields
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
| | - Thérèse A Holton
- Food for Health Ireland, ‡UCD Conway Institute of Biomolecular and Biomedical Research, §School of Medicine, ∥School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland
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Deglaire A, De Oliveira SC, Jardin J, Briard-Bion V, Emily M, Ménard O, Bourlieu C, Dupont D. Impact of human milk pasteurization on the kinetics of peptide release during in vitro dynamic term newborn digestion. Electrophoresis 2016; 37:1839-50. [DOI: 10.1002/elps.201500573] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/22/2016] [Accepted: 03/04/2016] [Indexed: 01/09/2023]
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Dallas DC, Guerrero A, Parker EA, Robinson RC, Gan J, German JB, Barile D, Lebrilla CB. Current peptidomics: applications, purification, identification, quantification, and functional analysis. Proteomics 2015; 15:1026-38. [PMID: 25429922 PMCID: PMC4371869 DOI: 10.1002/pmic.201400310] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/08/2014] [Accepted: 11/24/2014] [Indexed: 12/28/2022]
Abstract
Peptidomics is an emerging field branching from proteomics that targets endogenously produced protein fragments. Endogenous peptides are often functional within the body-and can be both beneficial and detrimental. This review covers the use of peptidomics in understanding digestion, and identifying functional peptides and biomarkers. Various techniques for peptide and glycopeptide extraction, both at analytical and preparative scales, and available options for peptide detection with MS are discussed. Current algorithms for peptide sequence determination, and both analytical and computational techniques for quantification are compared. Techniques for statistical analysis, sequence mapping, enzyme prediction, and peptide function, and structure prediction are explored.
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Affiliation(s)
- David C. Dallas
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Andres Guerrero
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Evan A. Parker
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Randall C. Robinson
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Junai Gan
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - J. Bruce German
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
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Pisanu S, Pagnozzi D, Pes M, Pirisi A, Roggio T, Uzzau S, Addis MF. Differences in the peptide profile of raw and pasteurised ovine milk cheese and implications for its bioactive potential. Int Dairy J 2015. [DOI: 10.1016/j.idairyj.2014.10.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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39
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Holton TA, Vijayakumar V, Dallas DC, Guerrero A, Borghese RA, Lebrilla CB, German JB, Barile D, Underwood MA, Shields DC, Khaldi N. Following the digestion of milk proteins from mother to baby. J Proteome Res 2014; 13:5777-83. [PMID: 25385259 PMCID: PMC4261950 DOI: 10.1021/pr5006907] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Little is known about the digestive process in infants. In particular, the chronological activity of enzymes across the course of digestion in the infant remains largely unknown. To create a temporal picture of how milk proteins are digested, enzyme activity was compared between intact human milk samples from three mothers and the gastric samples from each of their 4-12 day postpartum infants, 2 h after breast milk ingestion. The activities of 7 distinct enzymes are predicted in the infant stomach based on their observed cleavage pattern in peptidomics data. We found that the same patterns of cleavage were evident in both intact human milk and gastric milk samples, demonstrating that the enzyme activities that begin in milk persist in the infant stomach. However, the extent of enzyme activity is found to vary greatly between the intact milk and gastric samples. Overall, we observe that milk-specific proteins are cleaved at higher levels in the stomach compared to human milk. Notably, the enzymes we predict here only explain 78% of the cleavages uniquely observed in the gastric samples, highlighting that further investigation of the specific enzyme activities associated with digestion in infants is warranted.
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Affiliation(s)
- Thérèse A Holton
- UCD Conway Institute of Biomolecular and Biomedical Research/School of Medicine and Medical Sciences/UCD Complex and Adaptive Systems Laboratory, University College Dublin , Dublin 4, Republic of Ireland
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40
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Dallas DC, Weinborn V, de Moura Bell JMLN, Wang M, Parker EA, Guerrero A, Hettinga KA, Lebrilla CB, German JB, Barile D. Comprehensive peptidomic and glycomic evaluation reveals that sweet whey permeate from colostrum is a source of milk protein-derived peptides and oligosaccharides. Food Res Int 2014; 63:203-209. [PMID: 25284962 DOI: 10.1016/j.foodres.2014.03.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Whey permeate is a co-product obtained when cheese whey is passed through an ultrafiltration membrane to concentrate whey proteins. Whey proteins are retained by the membrane, whereas the low-molecular weight compounds such as lactose, salts, oligosaccharides and peptides pass through the membrane yielding whey permeate. Research shows that bovine milk from healthy cows contains hundreds of naturally occurring peptides - many of which are homologous with known antimicrobial and immunomodulatory peptides - and nearly 50 oligosaccharide compositions (not including structural isomers). As these endogenous peptides and oligosaccharides have low-molecular weight and whey permeate is currently an under-utilized product stream of the dairy industry, we hypothesized that whey permeate may serve as an inexpensive source of naturally occurring functional peptides and oligosaccharides. Laboratory fractionation of endogenous peptides and oligosaccharides from bovine colostrum sweet whey was expanded to pilot-scale. The membrane fractionation methodology used was similar to the methods commonly used industrially to produce whey protein concentrate and whey permeate. Pilot-scale fractionation was compared to laboratory-scale fractionation with regard to the identified peptides and oligosaccharide compositions. Results were interpreted on the basis of whether industrial whey permeate could eventually serve as a source of functional peptides and oligosaccharides. The majority (96%) of peptide sequences and the majority (96%) of oligosaccharide compositions found in the laboratory-scale process were mirrored in the pilot-scale process. Moreover, the pilot-scale process recovered an additional 33 peptides and 1 oligosaccharide not identified from the laboratory-scale extraction. Both laboratory- and pilot-scale processes yielded peptides deriving primarily from the protein β-casein. The similarity of the laboratory-and pilot-scale's resulting peptide and oligosaccharide profiles demonstrates that whey permeate can serve as an industrial-scale source of bovine milk peptides and oligosaccharides.
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Affiliation(s)
- David C Dallas
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States ; Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Valerie Weinborn
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Juliana M L N de Moura Bell
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Meng Wang
- Dairy Science and Technology Group, Food Quality and Design Group, Wageningen University, Bomenweg 2, Wageningen 6703HD, The Netherlands
| | - Evan A Parker
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Andres Guerrero
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Kasper A Hettinga
- Dairy Science and Technology Group, Food Quality and Design Group, Wageningen University, Bomenweg 2, Wageningen 6703HD, The Netherlands
| | - Carlito B Lebrilla
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States ; Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - J Bruce German
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States ; Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States ; Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
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Khaldi N, Vijayakumar V, Dallas D, Guerrero A, Wickramasinghe S, Smilowitz JT, Medrano JF, Lebrilla C, Shields DC, German JB. Predicting the important enzymes in human breast milk digestion. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:7225-7232. [PMID: 24620897 PMCID: PMC4264622 DOI: 10.1021/jf405601e] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/12/2014] [Accepted: 03/12/2014] [Indexed: 05/31/2023]
Abstract
Human milk is known to contain several proteases, but little is known about whether these enzymes are active, which proteins they cleave, and their relative contribution to milk protein digestion in vivo. This study analyzed the mass spectrometry-identified protein fragments found in pooled human milk by comparing their cleavage sites with the enzyme specificity patterns of an array of enzymes. The results indicate that several enzymes are actively taking part in the digestion of human milk proteins within the mammary gland, including plasmin and/or trypsin, elastase, cathepsin D, pepsin, chymotrypsin, a glutamyl endopeptidase-like enzyme, and proline endopeptidase. Two proteins were most affected by enzyme hydrolysis: β-casein and polymeric immunoglobulin receptor. In contrast, other highly abundant milk proteins such as α-lactalbumin and lactoferrin appear to have undergone no proteolytic cleavage. A peptide sequence containing a known antimicrobial peptide is released in breast milk by elastase and cathepsin D.
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Affiliation(s)
- Nora Khaldi
- Conway Institute of Biomolecular
and Biomedical Research, School
of Medicine and Medical Sciences and Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Republic of Ireland
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Vaishnavi Vijayakumar
- Conway Institute of Biomolecular
and Biomedical Research, School
of Medicine and Medical Sciences and Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Republic of Ireland
| | - David
C. Dallas
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Andrés Guerrero
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Saumya Wickramasinghe
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
- Department
of Basic Veterinary Sciences, University
of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Jennifer T. Smilowitz
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Juan F. Medrano
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Carlito
B. Lebrilla
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Denis C. Shields
- Conway Institute of Biomolecular
and Biomedical Research, School
of Medicine and Medical Sciences and Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Republic of Ireland
| | - J. Bruce German
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
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42
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Phelan M, Khaldi N, Shields DC, Kerins DM. Angiotensin converting enzyme and nitric oxide inhibitory activities of novel milk derived peptides. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2013.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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43
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Holton TA, Vijayakumar V, Khaldi N. Bioinformatics: Current perspectives and future directions for food and nutritional research facilitated by a Food-Wiki database. Trends Food Sci Technol 2013. [DOI: 10.1016/j.tifs.2013.08.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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44
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Mooney C, Haslam NJ, Holton TA, Pollastri G, Shields DC. PeptideLocator: prediction of bioactive peptides in protein sequences. Bioinformatics 2013; 29:1120-6. [DOI: 10.1093/bioinformatics/btt103] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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