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Vorob’ev MM, Açıkgöz BD, Güler G, Golovanov AV, Sinitsyna OV. Proteolysis of Micellar β-Casein by Trypsin: Secondary Structure Characterization and Kinetic Modeling at Different Enzyme Concentrations. Int J Mol Sci 2023; 24:ijms24043874. [PMID: 36835285 PMCID: PMC9960058 DOI: 10.3390/ijms24043874] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Tryptic proteolysis of protein micelles was studied using β-casein (β-CN) as an example. Hydrolysis of specific peptide bonds in β-CN leads to the degradation and rearrangement of the original micelles and the formation of new nanoparticles from their fragments. Samples of these nanoparticles dried on a mica surface were characterized by atomic force microscopy (AFM) when the proteolytic reaction had been stopped by tryptic inhibitor or by heating. The changes in the content of β-sheets, α-helices, and hydrolysis products during proteolysis were estimated by using Fourier-transform infrared (FTIR) spectroscopy. In the current study, a simple kinetic model with three successive stages is proposed to predict the rearrangement of nanoparticles and the formation of proteolysis products, as well as changes in the secondary structure during proteolysis at various enzyme concentrations. The model determines for which steps the rate constants are proportional to the enzyme concentration, and in which intermediate nano-components the protein secondary structure is retained and in which it is reduced. The model predictions were in agreement with the FTIR results for tryptic hydrolysis of β-CN at different concentrations of the enzyme.
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Affiliation(s)
- Mikhail M. Vorob’ev
- A.N. Nesmeyanov Institute of Organoelement Compounds, RAS, 28 ul. Vavilova, 119991 Moscow, Russia
- Correspondence:
| | - Burçin Dersu Açıkgöz
- Division of Bioengineering, Graduate School, Izmir University of Economics, Izmir 35330, Turkey
| | - Günnur Güler
- Biophysics Laboratory, Department of Physics, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
- Biomedical Bioengineering, Izmir University of Economics, Sakarya Cad., Izmir 35330, Turkey
| | - Andrey V. Golovanov
- A.N. Nesmeyanov Institute of Organoelement Compounds, RAS, 28 ul. Vavilova, 119991 Moscow, Russia
| | - Olga V. Sinitsyna
- A.N. Nesmeyanov Institute of Organoelement Compounds, RAS, 28 ul. Vavilova, 119991 Moscow, Russia
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Vorob'ev MM. Modeling of Proteolysis of β-Lactoglobulin and β-Casein by Trypsin with Consideration of Secondary Masking of Intermediate Polypeptides. Int J Mol Sci 2022; 23:ijms23158089. [PMID: 35897664 PMCID: PMC9331131 DOI: 10.3390/ijms23158089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023] Open
Abstract
The opening of protein substrates during degradation by proteases and the corresponding exposure of their internal peptide bonds for a successful enzymatic attack, the so-called demasking effect, was studied for β-lactoglobulin (β-LG) and β-casein (β-CN) hydrolyzed by trypsin. Demasking was estimated by monitoring the redshift in intrinsic tryptophan fluorescence, characterizing the accessibility of polypeptide chains to aqueous medium. The secondary masking of intermediate polypeptides, giving an inverse effect to demasking, caused a restriction of the substrate opening. This led to the limitations in the red shift of fluorescence and the degree of hydrolysis with a long time of hydrolysis of β-LG and β-CN at a constant substrate concentration and reduced trypsin concentrations. The proposed proteolysis model included demasking of initially masked bonds in the protein globule or micelle, secondary masking of intermediate polypeptides, and their subsequent slow demasking. The hydrolysis of peptide bonds was modeled taking into account different hydrolysis rate constants for different peptide bonds. It was demonstrated that demasking competes with secondary masking, which is less noticeable at high trypsin concentrations. Modeling of proteolysis taking into account two demasking processes and secondary masking made it possible to simulate kinetic curves consistent with the experimental data.
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Affiliation(s)
- Mikhail M Vorob'ev
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 ul. Vavilova, 119991 Moscow, Russia
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Demasking kinetics of peptide bond cleavage for whey protein isolate hydrolysed by Bacillus licheniformis protease. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2017.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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4
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Determination of kinetic parameters for casein hydrolysis by chymotrypsin using two ranges of substrate concentration. Int Dairy J 2016. [DOI: 10.1016/j.idairyj.2016.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Broyard C, Gaucheron F. Modifications of structures and functions of caseins: a scientific and technological challenge. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13594-015-0220-y] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Vorob’ev MM. Quantification of two-step proteolysis model with consecutive demasking and hydrolysis of peptide bonds using casein hydrolysis by chymotrypsin. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.02.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Fynbo CH, Lorentsen RH, Etzerodt M, Thøgersen HC, Holtet TL. Characterization of a recombinant granzyme B derivative as a “restriction” protease. Protein Expr Purif 2005; 39:209-18. [PMID: 15642472 DOI: 10.1016/j.pep.2004.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Revised: 10/16/2004] [Indexed: 11/19/2022]
Abstract
Blood coagulation factor Xa (FXa) and Thrombin are well-known serine proteases often used for processing of recombinant fusion proteins, but because they are purified from bovine blood or other animal sources, there is a risk of pathogenic contaminants in the preparation of the proteases. We report here the characterization of a recombinant serine protease produced in Escherichia coli, which can be used as a specific and efficient alternative to FXa and Thrombin as processing protease. This recombinant protease is derived from human granzyme B (GrB). The protease is found to be very stable in general, and it performs very well in the cleavage of several different fusion proteins tested and was even found superior to processing by FXa in two cases.
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Affiliation(s)
- Charlotte Harkjaer Fynbo
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark.
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Komissarov AA, Declerck PJ, Shore JD. Protonation State of a Single Histidine Residue Contributes Significantly to the Kinetics of the Reaction of Plasminogen Activator Inhibitor-1 with Tissue-type Plasminogen Activator. J Biol Chem 2004; 279:23007-13. [PMID: 15033993 DOI: 10.1074/jbc.m401383200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Stopped-flow fluorometry was used to study the kinetics of the reactive center loop insertion occurring during the reaction of N-((2-(iodoacetoxy)ethyl)-N-methyl)amino-7-nitrobenz-2-oxa-3-diazole (NBD) P9 plasminogen activator inhibitor-1 (PAI-1) with tissue-(tPA) and urokinase (uPA)-type plasminogen activators and human pancreatic elastase at pH 5.5-8.5. The limiting rate constants of reactive center loop insertion (k(lim)) and concentrations of proteinase at half-saturation (K(0.5)) for tPA and uPA and the specificity constants (k(lim)/K(0.5)) for elastase were determined. The pH dependences of k(lim)/K(0.5) reflected inactivation of each enzyme due to protonation of His57 of the catalytic triad. However, the specificity of the inhibitory reaction with tPA and uPA was notably higher than that for the substrate reaction catalyzed by elastase. pH dependences of k(lim) and K(0.5) obtained for tPA revealed an additional ionizable group (pKa, 6.0-6.2) affecting the reaction. Protonation of this group resulted in a significant increase in both k(lim) and K(0.5) and a 4.6-fold decrease in the specificity of the reaction of tPA with NBD P9 PAI-1. Binding of monoclonal antibody MA-55F4C12 to PAI-1 induced a decrease in k(lim) and K(0.5) at any pH but did not affect either the pKa of the group or an observed decrease in k(lim)/K(0.5) due to protonation of the group. In contrast to tPA, the k(lim) and K(0.5) for the reactions of uPA with NBD P9 PAI-1 or its complex with the monoclonal antibody were independent of pH in the 6.5-8.5 range. Since slightly acidic pH is a feature of a number of malignant tumors, alterations in PAI-1/tPA kinetics could play a role in the cancerogenesis. Changes in the protonation state of His(188), which is placed closely to the S1 site and is unique for tPA, has been proposed to contribute to the observed pH dependences of k(lim) and K(0.5).
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Affiliation(s)
- Andrey A Komissarov
- Division of Biochemical Research, Department of Pathology, Henry Ford Health System, Detroit, Michigan 48202, USA.
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Chobert JM. Milk protein modification to improve functional and biological properties. ADVANCES IN FOOD AND NUTRITION RESEARCH 2003; 47:1-71. [PMID: 14639781 DOI: 10.1016/s1043-4526(03)47001-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Jean-Marc Chobert
- Laboratoire d'Etude des Interactions des Molécules Alimentaires Institut National de la Recherche Agronomique Rue de la Géraudière B.P. 71627, 44316 Nantés, France
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Yeh CM, Yang MC, Tsai YC. Application potency of engineered G159 mutants on P1 substrate pocket of subtilisin YaB as improved meat tenderizers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2002; 50:6199-6204. [PMID: 12358502 DOI: 10.1021/jf0256889] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A serine protease, subtilisin YaB, produced by alkalophilic Bacillus YaB, shows promises as a potent meat tenderizer, because its substrate specificity is for small amino acids, which are found at high levels in meat connective tissue proteins. Substrate specificity engineering of the substrate binding pockets was used to generate more suitable meat-tenderizing mutants, G124A, G124V, G159A, and G159S, derived from recombinant wild subtilisin YaB and expressed in Bacillus subtilis DB104. The characteristics of these recombinant enzymes were studied to evaluate their usefulness as improved meat tenderizers. The proteolytic activities of recombinant subtilisin YaB, engineered subtilisin YaBs, and commercially available papain, bromelain, collagenase, and elastase were compared using elastin, collagen, casein, and myofibrillar proteins as substrates. Hydrolysis of beef proteins was evaluated using the myofibrillar fragmentation index and collagen solubility. The results demonstrated that recombinant mutant G159A was the most improved meat tenderizer and can be used in the meat pH range of 5.5-6.0 and the temperature range of 10-50 degrees C. Contrary to the result obtained from artificial substrate, mutant enzymes engineered on G124 residues did not exhibit better tenderizing ability when elastin, collagen, or meat was used as substrate, suggesting the necessity of evaluation by real substrate before protein-engineered enzymes are applied commercially.
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Affiliation(s)
- Chuan-Mei Yeh
- Department of Food Science, National Chung-Hsing University, Taichung, Taiwan, Republic of China, and Institute of Biochemistry, National Yang-Ming University, Taipei, Taiwan, Republic of China
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Abstract
Apparent rate constants of tryptic hydrolysis of amide bonds containing Arg and Lys residues in beta-casein were determined by the analysis of kinetics of accumulation of 17 major peptide components revealed by high performance liquid chromatography. When studying pH influence on Arg/Lys bond cleavage preference, averaged rate constants over several Arg&bond;X and Lys&bond;X bonds were used for analysis of kinetics of wild-type trypsin, K188H, K188F, K188Y, K188W, and of K188D/D189K mutants. The pK(a1) value of 6.5 was found for all studied trypsins. For wild-type trypsin and its K188D/D189K mutant, pK(a2) was found to be 10. The lowest among studied engineered trypsins pK(a2) = 9.3 was determined for K188Y mutant. Considerable preference for the cleavage of Arg over Lys containing peptide bonds was demonstrated for all trypsins with engineered S2 site except for K188H and K188F. The comparison of individual rate constants for various bonds showed that during the hydrolysis by wild-type trypsin, the probabilities of splitting depend on secondary specificity and local hydrophobicity of amino acid residues, which are nearest to the hydrolyzed peptide bond (P2 site). The improvement of prediction of hydrolysis rates performed by the used program was achieved after considering the presence of hydrophobic neighborhood of Lys48--Ile49 and Arg202--Gly203 bonds.
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Affiliation(s)
- M M Vorob'ev
- Institute of Elementoorganic Compounds, RAS, Vavilova ul. 28, 117813, Moscow, Russia
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Villalonga R, Villalonga ML, Gómez L. Preparation and functional properties of trypsin modified by carboxymethylcellulose. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1381-1177(00)00003-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Gorfe AA, Brandsdal BO, Leiros HKS, Helland R, Smal�s AO. Electrostatics of mesophilic and psychrophilic trypsin isoenzymes: Qualitative evaluation of electrostatic differences at the substrate binding site. Proteins 2000. [DOI: 10.1002/(sici)1097-0134(20000801)40:2<207::aid-prot40>3.0.co;2-u] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Briand L, Chobert JM, Gantier R, Declerck N, Tran V, Léonil J, Mollé D, Haertlé T. Impact of the lysine-188 and aspartic acid-189 inversion on activity of trypsin. FEBS Lett 1999; 442:43-7. [PMID: 9923601 DOI: 10.1016/s0014-5793(98)01611-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The impact of the charge rearrangement on the specificity of trypsin was tested by an inversion of sequence K188D/D189K maintaining the integrity of the charges of the substrate binding pocket when switching their polarity. In native trypsin, aspartate 189 situated at the bottom of the primary substrate binding pocket interacts with arginine and lysine side chains of the substrate. The kinetic parameters of the wild-type trypsin and K188D/D189K mutant were determined with synthetic tetrapeptide substrates. Compared with trypsin, the mutant K188D/D189K exhibits a 1.5- to 6-fold increase in the Km for the substrates containing arginine and lysine, respectively. This mutant shows a approximately 30-fold decrease of its k(cat) and its second-order rate constant k(cat)/Km decreases approximately 40- and 150-fold for substrates containing arginine and lysine, respectively. Hence, trypsin K188D/D189K displays a large increase in preference for arginine over lysine.
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Affiliation(s)
- L Briand
- Institut National de la Recherche Agronomique, LEIMA, Nantes, France
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CHOBERT JEANMARC, BRIAND LOIC, HAERTLE THOMAS. INFLUENCE OF G187W/K188F/D189Y MUTATION IN THE SUBSTRATE BINDING POCKET OF TRYPSIN ON ?-CASEIN PROCESSING. J Food Biochem 1998. [DOI: 10.1111/j.1745-4514.1998.tb00260.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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