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Guo Y, Zhou J, Jia W, Gao H, Zhang H, Zhang C. Characterization of a Novel Milk-Clotting Aspartic Protease from Penicillium sp. and Structural Explanation for its High Milk-Clotting Index. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37017929 DOI: 10.1021/acs.jafc.2c07303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
A novel milk-clotting enzyme isolated from Penicillium sp. ACCC 39790 (PsMCE) was prepared by heterologous expression. The recombinant PsMCE had an apparent molecular mass of 45 kDa and exhibited maximum casein hydrolysis activity at pH 4.0 and 50 °C. The PsMCE activity was enhanced by calcium ions and strongly inhibited by pepstatin A. Through hydrolysis pattern and cleavage site analyses, the milk-clotting activity of PsMCE was related to its specific hydrolysis between Phe105 and Met106 in the κ-casein proteins. The structural basis of PsMCE was characterized using homology modeling, molecular docking, and interactional analysis. The P1' region of PsMCE is critical for its selective binding to the hydrolytic site in κ-casein, and the hydrophobic forces play a decisive role in the specific cleavage of Phe105 and Met106. These interactional analyses between PsMCE and the ligand peptide clarified the fundamentals of its high milk-clotting index (MCI). PsMCE could be applied in cheese making due to its thermolability and high MCI value as a potential milk-clotting enzyme.
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Affiliation(s)
- Yujie Guo
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Xinjiang Taikun Group Co., Ltd., Xinjiang Uygur Autonomous Region, Changji 831100, People's Republic of China
| | - Jiaojiao Zhou
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wei Jia
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Xinjiang Taikun Group Co., Ltd., Xinjiang Uygur Autonomous Region, Changji 831100, People's Republic of China
| | - Hongwei Gao
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Xinjiang Taikun Group Co., Ltd., Xinjiang Uygur Autonomous Region, Changji 831100, People's Republic of China
| | - Hongru Zhang
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chunhui Zhang
- Key Laboratory of Agro-Products Processing, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Balabova DV, Belenkaya SV, Volosnikova EA, Hermes T, Chirkova VY, Sharlaeva EA, Shcherbakov DN, Belov AN, Koval AD, Elchaninov VV. Can Recombinant Tree Shrew (Tupaia belangeri chinensis) Chymosin Coagulate Cow (Bos taurus) Milk? APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822060023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Abstract
Genetically engineered chymosin from the tree shrew (Tupaia belangeri chinensis) has been obtained and partially characterized for the first time. The target enzyme was produced in Escherichia coli, strain BL21(DE3). It was shown that tree shrew recombinant chymosin coagulates cow milk (Bos taurus). The total and specific milk-clotting activity of the obtained enzyme was 0.7–5.3 IMCU/mL and 8.8–16.6 IMCU/mg. The nonspecific proteolytic activity of tree shrew recombinant chymosin in relation to total bovine casein was 30 and 117% higher than that of recombinant chymosin of cow and of single-humped camel respectively. It was found that in comparison with most of the known genetically engineered chymosins, the tree shrew enzyme showed exceptionally low thermal stability. After heating at 45°C, the coagulation ability of tree shrew recombinant chymosin decreased by more than 40%, and at 50°C the enzyme lost more than 90% of the initial milk-clotting activity. The Michaelis constant (Km), enzyme turnover number (kcat), and catalytic efficiency (kcat/Km) for genetically engineered chymosin from the tree shrew were 6.3 ± 0.1 µM, 11 927 ± 3169 s–1 and 1968 ± 620 µM–1 s–1, respectively. Comparative analysis showed that the primary structure of the chymosin-sensitive site of cow kappa-casein and the supposed similar sequence of tree shrew kappa-casein differed by 75%. The ability of tree shrew recombinant chymosin to coagulate cow’s milk, along with a low thermal stability and high catalytic efficiency with respect to the substrate, imitating the chymosin-sensitive site of cow kappa-casein, suggests that this enzyme is of potential interest for cheese making.
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Liu X, Peng L, Zhang JZH. Accurate and Efficient Calculation of Protein–Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants. J Chem Inf Model 2018; 59:272-281. [DOI: 10.1021/acs.jcim.8b00248] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Xiao Liu
- State Key Laboratory for Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Long Peng
- State Key Laboratory for Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - John Z. H. Zhang
- State Key Laboratory for Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
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Chen F, Liu H, Sun H, Pan P, Li Y, Li D, Hou T. Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking. Phys Chem Chem Phys 2018; 18:22129-39. [PMID: 27444142 DOI: 10.1039/c6cp03670h] [Citation(s) in RCA: 309] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Understanding protein-protein interactions (PPIs) is quite important to elucidate crucial biological processes and even design compounds that interfere with PPIs with pharmaceutical significance. Protein-protein docking can afford the atomic structural details of protein-protein complexes, but the accurate prediction of the three-dimensional structures for protein-protein systems is still notoriously difficult due in part to the lack of an ideal scoring function for protein-protein docking. Compared with most scoring functions used in protein-protein docking, the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) methodologies are more theoretically rigorous, but their overall performance for the predictions of binding affinities and binding poses for protein-protein systems has not been systematically evaluated. In this study, we first evaluated the performance of MM/PBSA and MM/GBSA to predict the binding affinities for 46 protein-protein complexes. On the whole, different force fields, solvation models, and interior dielectric constants have obvious impacts on the prediction accuracy of MM/GBSA and MM/PBSA. The MM/GBSA calculations based on the ff02 force field, the GB model developed by Onufriev et al. and a low interior dielectric constant (εin = 1) yield the best correlation between the predicted binding affinities and the experimental data (rp = -0.647), which is better than MM/PBSA (rp = -0.523) and a number of empirical scoring functions used in protein-protein docking (rp = -0.141 to -0.529). Then, we examined the capability of MM/GBSA to identify the possible near-native binding structures from the decoys generated by ZDOCK for 43 protein-protein systems. The results illustrate that the MM/GBSA rescoring has better capability to distinguish the correct binding structures from the decoys than the ZDOCK scoring. Besides, the optimal interior dielectric constant of MM/GBSA for re-ranking docking poses may be determined by analyzing the characteristics of protein-protein binding interfaces. Considering the relatively high prediction accuracy and low computational cost, MM/GBSA may be a good choice for predicting the binding affinities and identifying correct binding structures for protein-protein systems.
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Affiliation(s)
- Fu Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Hui Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Huiyong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Peichen Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China. and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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Ansari SM, Sørensen J, Schiøtt B, Palmer DS. On the effect of mutations in bovine or camel chymosin on the thermodynamics of binding κ-caseins. Proteins 2018; 86:75-87. [DOI: 10.1002/prot.25410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/18/2017] [Accepted: 10/27/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Samiul M. Ansari
- Department of Pure and Applied Chemistry; University of Strathclyde, Thomas Graham Building, 295 Cathedral Street; Glasgow G1 1XL Scotland
| | - Jesper Sørensen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry; University of Aarhus, Langelandsgade 140; Aarhus DK 8000 Denmark
| | - Birgit Schiøtt
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry; University of Aarhus, Langelandsgade 140; Aarhus DK 8000 Denmark
| | - David S. Palmer
- Department of Pure and Applied Chemistry; University of Strathclyde, Thomas Graham Building, 295 Cathedral Street; Glasgow G1 1XL Scotland
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Ansari SM, Coletta A, Kirkeby Skeby K, Sørensen J, Schiøtt B, Palmer DS. Allosteric-Activation Mechanism of Bovine Chymosin Revealed by Bias-Exchange Metadynamics and Molecular Dynamics Simulations. J Phys Chem B 2016; 120:10453-10462. [PMID: 27628309 DOI: 10.1021/acs.jpcb.6b07491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aspartic protease, bovine chymosin, catalyzes the proteolysis of κ-casein proteins in milk. The bovine chymosin-κ-casein complex is of industrial interest as the enzyme is used extensively in the manufacturing of processed dairy products. The apo form of the enzyme adopts a self-inhibited conformation in which the side chain of Tyr77 occludes the binding site. On the basis of kinetic, mutagenesis, and crystallographic data, it has been widely reported that a HPHPH sequence in the P8-P4 residues of the natural substrate κ-casein acts as the allosteric activator, but the mechanism by which this occurs has not previously been elucidated due to the challenges associated with studying this process by experimental methods. Here we have employed two computational techniques, molecular dynamics and bias-exchange metadynamics simulations, to study the mechanism of allosteric activation and to compute the free energy surface for the process. The simulations reveal that allosteric activation is initiated by interactions between the HPHPH sequence of κ-casein and a small α-helical region of chymosin (residues 112-116). A small conformational change in the α-helix causes the side chain of Phe114 to vacate a pocket that may then be occupied by the side chain of Tyr77. The free energy surface for the self-inhibited to open transition is significantly altered by the presence of the HPHPH sequence of κ-casein.
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Affiliation(s)
- Samiul M Ansari
- Department of Pure and Applied Chemistry, University of Strathclyde , Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
| | - Andrea Coletta
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Katrine Kirkeby Skeby
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Jesper Sørensen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - David S Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde , Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
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Ratkova EL, Palmer DS, Fedorov MV. Solvation thermodynamics of organic molecules by the molecular integral equation theory: approaching chemical accuracy. Chem Rev 2015; 115:6312-56. [PMID: 26073187 DOI: 10.1021/cr5000283] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ekaterina L Ratkova
- †G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia.,‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany
| | - David S Palmer
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,§Department of Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, United Kingdom
| | - Maxim V Fedorov
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,∥Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde, John Anderson Building, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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Bernhardt NA, Berhanu WM, Hansmann UHE. Mutations and seeding of amylin fibril-like oligomers. J Phys Chem B 2013; 117:16076-85. [PMID: 24294935 DOI: 10.1021/jp409777p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Seeding a protein solution with preformed fibrils can dramatically enhance the growth rate of amyloids. As the seeds do not need to be of the same protein, seeding may account for the observed correlations between amyloid diseases. In an effort to understand better the molecular mechanisms behind cross seeding we have studied in silico the effect of mutations on the seeding of amylin fibrils. Our investigations of the structural stability of decamers of wild type amylin peptides, of Y37L mutants, and of heteroassemblies of wild-type and mutant amylin molecules show that the experimentally observed efficient cross seeding can be explained based on similarity in fibril structure of components. We find that amyloids with similar side chains packing at the β-sheet interface are structurally compatible, acting as a good template for the congruent incorporation of homologues peptides. In the Y37L mutants, lack of tyrosine-specific interactions causes significant higher flexibility of the C terminal than observed in the wild-type fibril. This effects elongation of the mutant fibril leading to the longer lag times during aggregation that are observed in experiments. Our study gives guidelines for the design of ligands that could stabilize amylin fibrils.
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Affiliation(s)
- Nathan A Bernhardt
- Department of Biology, Southwestern Oklahoma State University , Weatherford, Oklahoma 73096, United States
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Palmer DS, Sørensen J, Schiøtt B, Fedorov MV. Solvent Binding Analysis and Computational Alanine Scanning of the Bovine Chymosin–Bovine κ-Casein Complex Using Molecular Integral Equation Theory. J Chem Theory Comput 2013; 9:5706-17. [DOI: 10.1021/ct400605x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David S. Palmer
- Department
of Physics, University of Strathclyde, John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
| | - Jesper Sørensen
- Department
of Chemistry and Biochemistry, University of California, San Diego, Urey Hall, 9500 Gilman Drive, La Jolla, California 92093, United States
- The
Center for Insoluble Protein Structures (inSPIN) and the Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Birgit Schiøtt
- The
Center for Insoluble Protein Structures (inSPIN) and the Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Maxim V. Fedorov
- Department
of Physics, University of Strathclyde, John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
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