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Korpela B, Pitkänen L, Heinonen M. Enzymatic modification of oat globulin enables covalent interaction with procyanidin B2. Food Chem 2022; 395:133568. [DOI: 10.1016/j.foodchem.2022.133568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 05/17/2022] [Accepted: 06/21/2022] [Indexed: 11/30/2022]
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Tóth A, Demcsák A, Zankl F, Oracz G, Unger LS, Bugert P, Laumen H, Párniczky A, Hegyi P, Rosendahl J, Gambin T, Płoski R, Koziel D, Gluszek S, Lindgren F, Löhr JM, Sahin-Tóth M, Witt H, Rygiel AM, Ewers M, Hegyi E. Loss-of-function variant in chymotrypsin like elastase 3B (CELA3B) is associated with non-alcoholic chronic pancreatitis. Pancreatology 2022; 22:713-718. [PMID: 35773178 PMCID: PMC9474678 DOI: 10.1016/j.pan.2022.06.258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/20/2022] [Accepted: 06/19/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Genetic alterations in digestive enzymes have been associated with chronic pancreatitis (CP). Recently, chymotrypsin like elastase 3B (CELA3B) emerged as a novel risk gene. Thus, we evaluated CELA3B in two European cohorts with CP. METHODS We analyzed all 8 CELA3B exons in 550 German non-alcoholic CP (NACP) patients and in 241 German controls by targeted DNA sequencing. In addition, we analyzed exons 6 and 7 by Sanger sequencing and the c.129+1G>A variant by melting curve analysis in 1078 further German controls. As replication cohort, we investigated up to 243 non-German European NACP patients and up to 1665 controls originating from Poland, Hungary, and Sweden. We assessed the cellular secretion and the elastase activity of recombinant CELA3B variants. RESULTS In the German discovery cohort, we detected a splice-site variant in intron 2, c.129+1G>A, in 9/550 (1.64%) CP patients and in 5/1319 (0.38%) controls (P=0.007, OR=4.4, 95% CI=1.5-13.0). In the European replication cohort, this variant was also enriched in patients (9/178 [5.06%]) versus controls (13/1247 [1.04%]) (P=0.001, OR=5.1, 95% CI=2.1-12.0). We did not find the two previously reported codon 90 variants, p.R90C and p.R90L. CONCLUSIONS Our data indicate that CELA3B is a susceptibility gene for CP. In contrast to previous reports suggesting that increased CELA3B activity is associated with CP risk, the splice-site variant identified here is predicted to cause diminished CELA3B expression. How reduced CELA3B function predisposes to pancreatitis remains to be elucidated.
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Affiliation(s)
- Andrea Tóth
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany
| | - Alexandra Demcsák
- Center for Exocrine Disorders, Department of Molecular and Cell Biology, Boston University, Henry M. Goldman School of Dental Medicine, Boston, MA, 02118, United States; Department of Surgery, University of California Los Angeles, Los Angeles, CA, 90095, United States
| | - Florence Zankl
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany
| | - Grzegorz Oracz
- Department of Gastroenterology, Hepatology, Feeding Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Lara Sophie Unger
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Service of Baden-Württemberg, Mannheim, Germany
| | - Helmut Laumen
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany; Department of Internal Medicine I, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Andrea Párniczky
- Heim Pál National Pediatric Institute, Budapest, Hungary; Institute for Translational Medicine, Medical School, Szentágothai Research Center, University of Pécs, Pécs, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Péter Hegyi
- Institute for Translational Medicine, Medical School, Szentágothai Research Center, University of Pécs, Pécs, Hungary; Center for Translational Medicine, Semmelweis University, Budapest, Hungary; Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Jonas Rosendahl
- Department of Internal Medicine I, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Dorota Koziel
- Collegium Medicum, Jan Kochanowski University of Kielce, Poland
| | | | - Fredrik Lindgren
- Department of Pediatric, Karolinska University Hospital, Stockholm, Sweden
| | - J Matthias Löhr
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Miklós Sahin-Tóth
- Center for Exocrine Disorders, Department of Molecular and Cell Biology, Boston University, Henry M. Goldman School of Dental Medicine, Boston, MA, 02118, United States; Department of Surgery, University of California Los Angeles, Los Angeles, CA, 90095, United States
| | - Heiko Witt
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany
| | | | - Maren Ewers
- Pediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany.
| | - Eszter Hegyi
- Center for Exocrine Disorders, Department of Molecular and Cell Biology, Boston University, Henry M. Goldman School of Dental Medicine, Boston, MA, 02118, United States; Institute for Translational Medicine, Medical School, Szentágothai Research Center, University of Pécs, Pécs, Hungary.
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Li X, Guo W, Xu R, Song Z, Ni T. The interaction mechanism between gold nanoparticles and proteins: Lysozyme, trypsin, pepsin, γ-globulin, and hemoglobin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 272:120983. [PMID: 35149482 DOI: 10.1016/j.saa.2022.120983] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
In this study, the interaction between gold nanoparticles (AuNPs) and proteins (including lysozyme, trypsin, pepsin, γ-globulin and hemoglobin) was investigated by UV-visible absorption spectroscopy, fluorescence spectroscopy, circular dichroism (CD) spectroscopy and protein activity assay. AuNPs was synthesized using reduction of HAuCl4 with sodium citrate. The formation of AuNPs was confirmed from the characteristic surface plasmon resonance band at 521 nm and transmission electron microscopy revealed the average particle size was about 10 nm. The results reveal that AuNPs can interact with proteins to form a "protein corona (PC)", but the protein concentration required to form a relatively stable PC is not the same. The quenching mechanism of proteins by AuNPs is arisen from static quenching. The binding constants of AuNPs with proteins are in the range from 106 to 1010 L mol-1, and the order is pepsin > γ-globulin > hemoglobin > trypsin > lysozyme at 298 K. Van der Waals forces and hydrogen bonds are the main forces for the lysozyme-AuNPs system. The interaction between trypsin/pepsin/γ-globulin/hemoglobin and AuNPs is mainly by hydrophobic interaction. The addition of AuNPs has an effect on the secondary structure of proteins as confirmed from CD spectra. The change in secondary structure of different proteins is different and seems to have little relation with the binding constant. The activity of lysozyme/trypsin/pepsin decreases with the addition of AuNPs.
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Affiliation(s)
- Xiangrong Li
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China.
| | - Wei Guo
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Ruonan Xu
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Zhizhi Song
- Grade 2020, Clinical Medicine, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Tianjun Ni
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
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Zhang Y, Yang R, Wang L, Li Y, Han J, Yang Y, Zheng H, Lu M, Shen Y, Yang H. Purification and characterization of a novel thermostable anticoagulant protein from medicinal leech Whitmania pigra Whitman. JOURNAL OF ETHNOPHARMACOLOGY 2022; 288:114990. [PMID: 35032585 DOI: 10.1016/j.jep.2022.114990] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/27/2021] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The prevalence of cardiovascular disease (CVD) is increasing worldwide. Despite significant improvements in novel targeted treatment agents, natural products purified from medicinal animals with minimal side effects have attracted much attention. Several native proteins explored from suck-blood leeches, such as non-thermostable hirudin and its variants, revealed potent anticoagulant activity. Traditional Chinese medicine clinics have proved that non-suck-blood leech Whitmania pigra Whitman (W. pigra) also played notable roles in CVD treatments even after decoction. However, only a few natural proteins and peptides have been identified from the fresh material of this medicinal species. AIM OF THE STUDY We aimed to purify and characterize thermostable anticoagulant proteins from W. pigra for further development of a therapeutic agent for thrombosis. MATERIALS AND METHODS W. pigra crude extract was prepared by decoction in water. Anticoagulant proteins were purified by DEAE cellulose DE-52, Sephadex G-75, and reversed-phase liquid chromatography sequentially and analyzed by SDS-PAGE and LC-MS/MS for structural information. In addition, we conducted in vitro anticoagulant experiments, including plasma recalcification time (PRT) assay, fibrinolytic assay, activated partial thromboplastin time (APTT), prothrombin time (PT), thrombin time (TT), fibrinogen (Fib) assay, and cell viability assays. Furthermore, a carrageenan-induced chronic thromboembolism model was employed in ICR mice, and four coagulation factors (APTT, PT, TT, and Fib) activities were determined after intragastric administration. RESULTS The anticoagulant protein WP-77 has a relative molecular weight of ca. 20.8 kDa. It was effective over a broad temperature range from 20 °C to 100 °C and a pH 2-8 condition. The anticoagulant activity of WP-77 was retained after incubation with pepsin but was greatly inhibited by trypsin (P < 0.01). It significantly prolonged APTT and TT (P < 0.05) but had little effect on PT and Fib in vitro. Furthermore, WP-77 of a low concentration resulted in the recovery of injured EA.hy926 by thrombin. The protein also significantly prolonged APTT and TT (P < 0.01) and inhibited thrombus formation in carrageenan-induced thrombosis mice, demonstrating its antithrombotic effect in vivo. CONCLUSION Our results suggest that WP-77 from W. pigra plays a distinct role in treating thrombotic diseases, and it is an essential substance of anticoagulant activity of non-suck-blood medicinal leeches. This thermostable anticoagulant protein could be a promising candidate for the development of clinical antithrombosis medicines.
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Affiliation(s)
- Yajie Zhang
- Department of Chinese Materia Medica and Pharmacy, School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
| | - Rong Yang
- Department of Chinese Materia Medica and Pharmacy, School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
| | - Liwei Wang
- Department of Chinese Materia Medica and Pharmacy, School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
| | - Ye Li
- Department of Chinese Materia Medica and Pharmacy, School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
| | - Jing Han
- Department of Chinese Materia Medica and Pharmacy, School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
| | - Yaya Yang
- Department of Chinese Materia Medica and Pharmacy, School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
| | - Hanxue Zheng
- Department of Chinese Materia Medica and Pharmacy, School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
| | - Mengyao Lu
- Department of Chinese Materia Medica and Pharmacy, School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
| | - Yuping Shen
- Department of Chinese Materia Medica and Pharmacy, School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
| | - Huan Yang
- Department of Chinese Materia Medica and Pharmacy, School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
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Li X, Liu H, Wu X, Xu R, Ma X, Zhang C, Song Z, Peng Y, Ni T, Xu Y. Exploring the interactions of naringenin and naringin with trypsin and pepsin: Experimental and computational modeling approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 258:119859. [PMID: 33957444 DOI: 10.1016/j.saa.2021.119859] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/11/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Naringenin and naringin are two natural compounds with important health benefits, whether as food or drug. It is necessary to study the interactions between naringenin/naringin and digestive proteases, such as trypsin and pepsin. In this study, the bindings of naringenin and naringin to trypsin and pepsin were investigated using multi-spectroscopy analysis and computational modeling approaches. Fluorescence experiments indicate that both naringenin and naringin can quench the intrinsic fluorescence of trypsin/pepsin via static quenching mechanism. Naringin binds trypsin/pepsin in a more firmly way than naringenin. Thermodynamic analysis reveals that the interactions of naringenin/naringin and trypsin/pepsin are synergistically driven by enthalpy and entropy, and the major driving forces are hydrophobic, electrostatic interactions and hydrogen bonding. Synchronous fluorescence spectroscopy, circular dichroism spectroscopy and FT-IR show that naringenin/naringin may induce microenvironmental and conformational changes of trypsin and pepsin. Molecular docking reveals that naringenin binds in the close vicinity of the active site (Ser-195) of trypsin and Asp-32 (the catalytic activity of pepsin) appears in naringin-pepsin system. The direct interactions between naringenin or naringin and catalytic amino acid residues will inhibit the catalytic activity of trypsin and pepsin, respectively. The results of molecular dynamic simulation validate the reliability of the docking results.
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Affiliation(s)
- Xiangrong Li
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Hongyi Liu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Xinzhe Wu
- Grade 2020, Clinical Medicine, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Ruonan Xu
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Xiaoyi Ma
- Grade 2018, Pharmaceutics, School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Congxiao Zhang
- Grade 2018, Pharmaceutics, School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Zhizhi Song
- Grade 2020, Clinical Medicine, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Yanru Peng
- Grade 2017, Clinical Pharmacy, School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Tianjun Ni
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Yongtao Xu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, Henan 453003, PR China.
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A Study of the Interaction, Morphology, and Structure in Trypsin-Epigallocatechin-3-Gallate Complexes. Molecules 2021; 26:molecules26154567. [PMID: 34361715 PMCID: PMC8348591 DOI: 10.3390/molecules26154567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 11/29/2022] Open
Abstract
Understanding the interaction between proteins and polyphenols is of significance to food industries. The aim of this research was to investigate the mode of aggregation for trypsin-EGCG (Epigallocatechin-3-gallate) complexes. For this, the complex was characterized by fluorescence spectroscopy, circular dichroism (CD) spectra, small-angel X-ray scattering (SAXS), and atomic force microscope (AFM) techniques. The results showed that the fluorescence intensity of trypsin-EGCG complexes decreased with increasing the concentration of EGCG, indicating that the interaction between trypsin and EGCG resulted in changes in the microenvironment around fluorescent amino acid residues. The results of CD analysis showed conformational changes in trypsin after binding with EGCG. The results from SAXS analysis showed that the addition of EGCG results in the formation of aggregates of trypsin-EGCG complexes, and increasing the concentration of EGCG resulted in larger aggregates. AFM images showed that the trypsin-EGCG complex formed aggregates of irregular ellipsoidal shapes with the size of about 200 × 400 × 200 nm, with EGCG interconnecting the trypsin particles. Overall, according to these results, it was concluded that the large aggregates of trypsin-EGCG complexes are formed from several small aggregates that are interconnected. The results of this study shed some light on the interaction between digestive enzymes and EGCG.
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Di Cera E. Mechanisms of ligand binding. BIOPHYSICS REVIEWS 2020; 1:011303. [PMID: 33313600 PMCID: PMC7714259 DOI: 10.1063/5.0020997] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022]
Abstract
Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.
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Affiliation(s)
- Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
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Liposomal/Nanoliposomal Encapsulation of Food-Relevant Enzymes and Their Application in the Food Industry. FOOD BIOPROCESS TECH 2020. [DOI: 10.1007/s11947-020-02513-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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On-line immobilized trypsin microreactor for evaluating inhibitory activity of phenolic acids by capillary electrophoresis and molecular docking. Food Chem 2019; 310:125823. [PMID: 31757489 DOI: 10.1016/j.foodchem.2019.125823] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 10/18/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022]
Abstract
Phenolic acids, which are important aromatic secondary metabolites, are widely distributed in plant foods. In this study, a simple, economical and fast on-line immobilized trypsin microreactor was developed for evaluating the inhibitory activity of phenolic acids by capillary electrophoresis. The Michaelis-Menten constant (Km) of immobilized trypsin was determined as 0.99 mM, and the half-maximal inhibitory concentration (IC50) and inhibition constant (Ki) of benzamidine were measured as 3.39 and 1.68 mM, respectively. Then, the developed strategy was applied to investigate the inhibitory activity of six phenolic acids on trypsin. The results showed that gallic acid, caffeic acid and ferulic acid had high inhibitory activity at concentration of 150 μM. Molecular docking results illustrated that gallic acid, caffeic acid and ferulic acid can interact indirectly with the catalytic and substrate-binding sites of trypsin. The developed strategy is an effective tool for evaluating inhibitory activity of phenolic acids on trypsin.
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Binding behaviors and kinetics studies on the interaction of silver nanoparticles with trypsin. Int J Biol Macromol 2018; 114:836-843. [DOI: 10.1016/j.ijbiomac.2018.03.172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 11/18/2022]
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The potential impact of carboxylic-functionalized multi-walled carbon nanotubes on trypsin: A Comprehensive spectroscopic and molecular dynamics simulation study. PLoS One 2018; 13:e0198519. [PMID: 29856868 PMCID: PMC5983559 DOI: 10.1371/journal.pone.0198519] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/21/2018] [Indexed: 01/03/2023] Open
Abstract
In this study, we report a detailed experimental, binding free energy calculation and molecular dynamics (MD) simulation investigation of the interactions of carboxylic-functionalized multi-walled carbon nanotubes (COOH-f-MWCNTs) with porcine trypsin (pTry). The enzyme exhibits decreased thermostability at 330K in the presence of COOH-f-MWCNTs. Furthermore, the activity of pTry also decreases in the presence of COOH-f-MWCNTs. The restricted diffusion of the substrate to the active site of the enzyme was observed in the experiment. The MD simulation analysis suggested that this could be because of the blocking of the S1 pocket of pTry, which plays a vital role in the substrate selectivity. The intrinsic fluorescence of pTry is quenched with increase in the COOH-f-MWCNTs concentration. Circular dichroism (CD) and UV–visible absorption spectroscopies indicate the ability of COOH-f-MWCNTs to experience conformational change in the native structure of the enzyme. The binding free energy calculations also show that electrostatics, π-cation, and π-π stacking interactions play important roles in the binding of the carboxylated CNTs with pTry. The MD simulation results demonstrated that the carboxylated CNTs adsorb to the enzyme stronger than the CNT without the–COOH groups. Our observations can provide an example of the nanoscale toxicity of COOH-f-MWCNTs for proteins, which is a critical issue for in vivo application of COOH-f-MWCNTs.
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Trypsin-Ligand binding affinities calculated using an effective interaction entropy method under polarized force field. Sci Rep 2017; 7:17708. [PMID: 29255159 PMCID: PMC5735144 DOI: 10.1038/s41598-017-17868-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/01/2017] [Indexed: 12/22/2022] Open
Abstract
Molecular dynamics (MD) simulation in the explicit water is performed to study the interaction mechanism of trypsin-ligand binding under the AMBER force field and polarized protein-specific charge (PPC) force field combined the new developed highly efficient interaction entropy (IE) method for calculation of entropy change. And the detailed analysis and comparison of the results of MD simulation for two trypsin-ligand systems show that the root-mean-square deviation (RMSD) of backbone atoms, B-factor, intra-protein and protein-ligand hydrogen bonds are more stable under PPC force field than AMBER force field. Our results demonstrate that the IE method is superior than the traditional normal mode (Nmode) method in the calculation of entropy change and the calculated binding free energy under the PPC force field combined with the IE method is more close to the experimental value than other three combinations (AMBER-Nmode, AMBER-IE and PPC-Nmode). And three critical hydrogen bonds between trypsin and ligand are broken under AMBER force field. However, they are well preserved under PPC force field. Detailed binding interactions of ligands with trypsin are further analyzed. The present work demonstrates that the polarized force field combined the highly efficient IE method is critical in MD simulation and free energy calculation.
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Salar S, Mehrnejad F, Sajedi RH, Arough JM. Chitosan nanoparticles-trypsin interactions: Bio-physicochemical and molecular dynamics simulation studies. Int J Biol Macromol 2017; 103:902-909. [DOI: 10.1016/j.ijbiomac.2017.05.140] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/20/2017] [Accepted: 05/23/2017] [Indexed: 01/31/2023]
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14
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Chi Z, Zhao J, Li W, Araghi A, Tan S. In vitro assessment of phthalate acid esters-trypsin complex formation. CHEMOSPHERE 2017; 185:29-35. [PMID: 28683334 DOI: 10.1016/j.chemosphere.2017.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 06/08/2017] [Accepted: 07/01/2017] [Indexed: 06/07/2023]
Abstract
In this work, interactions of three phthalate acid esters (PAEs), including dimethyl phthalate (DMP), diethyl phthalate (DEP) and dibutyl phthalate (DBP), with trypsin have been studied in vitro, under simulated physiological conditions using multi-spectroscopic techniques and molecular modeling. The results show that these PAEs can bind to the trypsin, forming trypsin-PAEs complexes, mainly via hydrophobic interactions, with the affinity order of DMP > DEP > DBP. Binding to the PAEs is found to result in molecular deformation of trypsin. The modeling results suggest that only DBP can bind with the amino acid residues of the catalytic triad and S1 binding pocket of trypsin, leading to potential competitive enzyme inhibition.
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Affiliation(s)
- Zhenxing Chi
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, PR China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China; Guangzhou Key Laboratory of Environmental Exposure and Health, School of Environment, Jinan University, Guangzhou 510632, PR China.
| | - Jing Zhao
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, PR China
| | - Weiguo Li
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, PR China
| | - Arash Araghi
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney 2006, Australia
| | - Songwen Tan
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, PR China
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Liu B, Xiao H, Li J, Geng S, Ma H, Liang G. Interaction of phenolic acids with trypsin: Experimental and molecular modeling studies. Food Chem 2017; 228:1-6. [PMID: 28317701 DOI: 10.1016/j.foodchem.2017.01.126] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 01/10/2017] [Accepted: 01/26/2017] [Indexed: 01/15/2023]
Abstract
Trypsin is a kind of protease for digestion and food processing, whose activity can be inhibited by phenolic acids in plant foods. However, most reports explained the inhibitory difference of phenolic acids based on the number and position of substituent groups, which failed to reveal the comprehensive inhibitory mechanism. In this work, the inhibitory effects of 11 common phenolic acids on trypsin were investigated. Amongst the tested cinnamic and benzoic acid derivatives, caffeic acid and gallic acid showed the strongest anti-trypsin activity with a noncompetitive inhibition pattern, respectively. The fluorescence analysis displayed that both the quenching rate constant (Kq) and binding constant (KA) of caffeic acid were higher than those of gallic acid. Molecular docking illustrated their different binding modes with trypsin. The ONIOM calculations revealed that the binding capacity of caffeic acid was higher than that of gallic acid, which could explain their difference in their inhibitory behaviors.
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Affiliation(s)
- Benguo Liu
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, PR China
| | - Huizhi Xiao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, School of Bioengineering, Chongqing University, Chongqing 400044, PR China
| | - Jiaqi Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, School of Bioengineering, Chongqing University, Chongqing 400044, PR China
| | - Sheng Geng
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, PR China
| | - Hanjun Ma
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, PR China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, School of Bioengineering, Chongqing University, Chongqing 400044, PR China.
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16
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Xiao F, Li W, Fang L, Wang D. Synthesis of akageneite (beta-FeOOH)/reduced graphene oxide nanocomposites for oxidative decomposition of 2-chlorophenol by Fenton-like reaction. JOURNAL OF HAZARDOUS MATERIALS 2016; 308:11-20. [PMID: 26808238 DOI: 10.1016/j.jhazmat.2016.01.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 06/05/2023]
Abstract
In this work, the composite of reduced graphene oxide and akageneite (Ak/rGO) was synthesised by co-precipitating and reduction processes. The morphological and structural features of the synthesized composites (Ak/rGO) were characterized by XRD, SEM, BET, FTIR, Zeta potential and XPS. The results revealed that (1) beta-FeOOH was successfully loaded on the reduced graphene oxide (rGO); (2) the presence of strong interfacial interactions (Fe-O-C bonds) between rGO and beta-FeOOH was observed; (3) the reduction of graphene oxide may be inhabited in the formation process of beta-FeOOH, producing rGO sheets rather than rGO sphere. In the heterogeneous Fenton-like reaction, the degradation rate constants of 2-chlorophenol (2-CP) increased 2-5 times after the addition of rGO probably due to the Fe-O-C bond. The increase of the content of rGO could contribute to the removal of 2-CP, due to the synergy of catalysis and 2-CP adsorption towards Ak/rGO. In this study, the Ak/rGO composite has exhibited great potential and significant prospects for environmental application.
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Affiliation(s)
- Feng Xiao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, No. 18, Shuangqing Road, Haidian District, Beijing 100085, China.
| | - Wentao Li
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, No. 18, Shuangqing Road, Haidian District, Beijing 100085, China
| | - Liping Fang
- Faculty of Material Science and Chemistry, China University of Geosciences, No. 388, Lumo Road, Wuhan 430074, China.
| | - Dongsheng Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, No. 18, Shuangqing Road, Haidian District, Beijing 100085, China
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17
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Probing the binding mechanisms of α-tocopherol to trypsin and pepsin using isothermal titration calorimetry, spectroscopic, and molecular modeling methods. J Biol Phys 2016; 42:415-34. [PMID: 27094449 DOI: 10.1007/s10867-016-9415-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 03/09/2016] [Indexed: 10/21/2022] Open
Abstract
α-Tocopherol is a required nutrient for a variety of biological functions. In this study, the binding of α-tocopherol to trypsin and pepsin was investigated using isothermal titration calorimetry (ITC), steady-state and time-resolved fluorescence measurements, circular dichroism (CD) spectroscopy, and molecular modeling methods. Thermodynamic investigations reveal that α-tocopherol binds to trypsin/pepsin is synergistically driven by enthalpy and entropy. The fluorescence experimental results indicate that α-tocopherol can quench the fluorescence of trypsin/pepsin through a static quenching mechanism. The binding ability of α-tocopherol with trypsin/pepsin is in the intermediate range, and one molecule of α-tocopherol combines with one molecule of trypsin/pepsin. As shown by circular dichroism (CD) spectroscopy, α-tocopherol may induce conformational changes of trypsin/pepsin. Molecular modeling displays the specific binding site and gives information about binding forces and α-tocopherol-tryptophan (Trp)/tyrosine (Tyr) distances. In addition, the inhibition rate of α-tocopherol on trypsin and pepsin was studied. The study provides a basic data set for clarifying the binding mechanisms of α-tocopherol with trypsin and pepsin and is helpful for understanding its biological activity in vivo.
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18
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Li X, Geng M. Probing the binding of procyanidin B3 to trypsin and pepsin: A multi-technique approach. Int J Biol Macromol 2016; 85:168-78. [DOI: 10.1016/j.ijbiomac.2015.12.075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 12/23/2022]
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19
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Ding K, Zhang H, Wang H, Lv X, Pan L, Zhang W, Zhuang S. Atomic-scale investigation of the interactions between tetrabromobisphenol A, tetrabromobisphenol S and bovine trypsin by spectroscopies and molecular dynamics simulations. JOURNAL OF HAZARDOUS MATERIALS 2015; 299:486-494. [PMID: 26252992 DOI: 10.1016/j.jhazmat.2015.07.050] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/01/2015] [Accepted: 07/18/2015] [Indexed: 06/04/2023]
Abstract
Tetrabromobisphenol A (TBBPA) and its replacement alternative tetrabromobisphenol S (TBBPS) are used widely as brominated flame retardants (BFRs). However, the potential risk of their effects on bovine trypsin remains largely unknown. We investigated the effects of TBBPA and TBBPS to bovine trypsin by the fluorescence spectroscopy, circular dichroism and molecular dynamics (MD) simulations. They statically quenched the intrinsic fluorescence of bovine trypsin in a concentration-dependent mode and caused slight red-shifted fluorescence. The short and long fluorescence lifetime decay components of bovine trypsin were both affected, partly due to the disturbed microenvironmental changes of Trp215. The β-sheet content of bovine trypsin was significantly reduced from 82.4% to 75.7% and 76.6% by TBBPA and TBBPS, respectively, possibly impairing the physiological function of bovine trypsin. TBBPA and TBBPS bind at the 8-anilinonaphthalene-1-sulfonate (ANS) binding site with an association constant of 1.09×10(4) M(-1) and 2.41×10(4) M(-1) at 298 K, respectively. MD simulations revealed that van der Waals interactions and hydrogen bond interactions are dominant for TBBPA, whereas electrostatic interactions are critical for TBBPS. Our in vitro and in silico studies are beneficial to the understanding of risk assessment and future design of environmental benign BFRs.
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Affiliation(s)
- Keke Ding
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huanxin Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Haifei Wang
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Xuan Lv
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Liumeng Pan
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Wenjing Zhang
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Shulin Zhuang
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
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20
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Discrimination between conformational selection and induced fit protein-ligand binding using Integrated Global Fit analysis. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 45:245-57. [PMID: 26538331 DOI: 10.1007/s00249-015-1090-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/07/2015] [Accepted: 10/13/2015] [Indexed: 02/07/2023]
Abstract
Molecular recognition between proteins and small molecule ligands is at the heart of biological function in cellular systems and the basis of modern rational drug development. Therefore, the mechanisms governing protein-ligand interaction have been objects of research for many decades. The last 15 years has seen a revival of a discussion whether conformational selection (CS) or induced fit (IF) is the most relevant binding mechanism. A decreasing observed rate constant, k obs, with increasing ligand concentration was considered to be a hallmark of CS, but according to contemporary knowledge, a positive saturating behavior of k obs can be explained by both CS and IF mechanisms. The only currently recognized kinetic method to differentiate between both binding mechanisms includes the measurement of two separate series of binding kinetics with variation of either protein or ligand under pseudo-first-order conditions. This study avoids the disadvantage of high protein concentrations and provides evidence that a comprehensive Integrated Global Fit analysis of sets of binding kinetics with just varied ligand concentration in combination with equilibrium data and optional displacement kinetics can effectively differentiate between CS and IF binding mechanisms. The limiting situation, when physical binding dominates over the previous (CS) or subsequent (IF) conformational changes, is carefully analyzed. Finally, the relevance of kinetic methods and the elucidation of more complex binding mechanisms are discussed for advanced rational selection and optimization of drug candidates.
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21
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Xiao H, Liu B, Mo H, Liang G. Comparative evaluation of tannic acid inhibiting α-glucosidase and trypsin. Food Res Int 2015; 76:605-610. [DOI: 10.1016/j.foodres.2015.07.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/07/2015] [Accepted: 07/19/2015] [Indexed: 10/23/2022]
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22
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Li X, Li P. Study on the interaction of β-carotene and astaxanthin with trypsin and pepsin by spectroscopic techniques. LUMINESCENCE 2015; 31:782-92. [DOI: 10.1002/bio.3024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/13/2015] [Accepted: 08/05/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Xiangrong Li
- Department of Chemistry, School of Basic Medicine; Xinxiang Medical University; Xinxiang Henan 453003 People's Republic of China
| | - Peihong Li
- The Clinical Skills Training Center; Xinxiang Medical University; Xinxiang Henan 453003 People's Republic of China
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23
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Li X, Yang Z. Dissection of the binding ofl-ascorbic acid to trypsin and pepsin using isothermal titration calorimetry, equilibrium microdialysis and spectrofluorimetry. RSC Adv 2015. [DOI: 10.1039/c5ra02592c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Clear and quantitative information on the nature ofl-ascorbic acid interaction with trypsin/pepsin should provide a firm base for its rational use in clinical practice.
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Affiliation(s)
- Xiangrong Li
- Department of Chemistry
- School of Basic Medicine
- Xinxiang Medical University
- Xinxiang
- P. R. China
| | - Zhijun Yang
- Department of Chemistry
- School of Basic Medicine
- Xinxiang Medical University
- Xinxiang
- P. R. China
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24
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Wang YQ, Tan CY, Zhuang SL, Zhai PZ, Cui Y, Zhou QH, Zhang HM, Fei Z. In vitro and in silico investigations of the binding interactions between chlorophenols and trypsin. JOURNAL OF HAZARDOUS MATERIALS 2014; 278:55-65. [PMID: 24953936 DOI: 10.1016/j.jhazmat.2014.05.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 06/03/2023]
Abstract
Being the first-degree toxic pollutants, chlorophenols (CP) have potential carcinogenic and mutagenic activity and toxicity. Since there still lacks studies on molecular interactions of chlorophenols with trypsin, one major binding target of many exogenous environmental pollutants, the binding interactions between five chlorophenols, 2-CP, 2,6-DCP, 2,4,6-TCP, 2,4,6-TCP, 2,3,4,6-TCP and PCP and trypsin were characterized by the combination of multispectroscopic techniques and molecular modeling. The chlorophenols bind at the one main site of trypsin and the binding induces the changes of microenvironment and global conformations of trypsin. Different number of chloride atoms significantly affects the binding and the binding constants KA ranks as KA (2-CP) < KA (2,6-DCP) ≈ KA (2,4,6-TCP) < KA (2,3,4,6-TCP) < KA (PCP). These chlorophenols interacts with trypsin mainly through hydrophobic interactions and via hydrogen bonding interactions and aromatic-aromatic π-π stacking interaction. Our results offer insights into the binding mechanism of chlorophenols with trypsin and provide important information for possible toxicity risk of chlorophenols to human health.
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Affiliation(s)
- Yan-Qing Wang
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City 224002, Jiangsu Province, People's Republic of China; Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province, People's Republic of China.
| | - Chun-Yun Tan
- Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province, People's Republic of China
| | - Shu-Lin Zhuang
- Institute of Environmental Science, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Peng-Zhan Zhai
- Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province, People's Republic of China
| | - Yun Cui
- Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province, People's Republic of China
| | - Qiu-Hua Zhou
- Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province, People's Republic of China
| | - Hong-Mei Zhang
- Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province, People's Republic of China
| | - Zhenghao Fei
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City 224002, Jiangsu Province, People's Republic of China; Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province, People's Republic of China
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25
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Plant cyclopropylsterol-cycloisomerase: key amino acids affecting activity and substrate specificity. Biochem J 2014; 459:289-99. [PMID: 24483781 DOI: 10.1042/bj20131239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The enzyme CPI (cyclopropylsterol-cycloisomerase) from the plant sterol pathway catalyses the cleavage of the 9β,19-cyclopropane ring of the 4α-methyl-cyclopropylsterol cycloeucalenol to produce the Δ8-sterol obtusifoliol. Randomly mutated plasmids carrying the Arabidopsis thaliana cpi gene were screened for inactive CPI mutant enzymes on the basis of their ability to genetically complement a Saccharomyces cerevisiae erg7 (defective in oxidosqualene cyclase) ergosterol auxotroph grown in the presence of exogenous cycloeucalenol, and led to the identification of four catalytically important residues. Site-directed mutagenesis experiments confirmed the role of the identified residues, and demonstrated the importance of selected acidic residues and a conserved G108NYFWTHYFF117 motif. The mutated isomerases were assayed both in vivo by quantification of cycloeucalenol conversion into ergosterol in erg7 cells, and in vitro by examination of activities of recombinant AtCPI (A. thaliana CPI) mutants. These studies show that Gly28, Glu29, Gly108 and Asp260 are crucial for CPI activity and that an hydroxy function at residue 113 is needed for maximal substrate affinity and CPI activity. CPI is inactive on upstream 4α,β-dimethyl-cyclopropylsterol precursors of phytosterols. The single mutation W112L generates a CPI with an extended substrate specificity, that is able to convert 4α,β-dimethyl-cyclopropylsterols into the corresponding Δ8 products. These findings provide insights into the molecular basis of CPI activity and substrate specificity.
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26
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Zhang H, Zhou Q, Cao J, Wang Y. Mechanism of cinnamic acid-induced trypsin inhibition: a multi-technique approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 116:251-257. [PMID: 23954540 DOI: 10.1016/j.saa.2013.07.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 07/10/2013] [Accepted: 07/21/2013] [Indexed: 06/02/2023]
Abstract
In order to investigate the association of the protease trypsin with cinnamic acid, the interaction was characterized by using fluorescence, UV-vis absorption spectroscopy, molecular modeling and an enzymatic inhibition assay. The binding process may be outlined as follows: cinnamic acid can interact with trypsin with one binding site to form cinnamic acid-trypsin complex, resulting in inhibition of trypsin activity; the spectroscopic data show that the interaction is a spontaneous process with the estimated enthalpy and entropy changes being -8.95 kJ mol(-1) and 50.70 J mol(-1) K(-1), respectively. Noncovalent interactions make the main contribution to stabilize the trypsin-cinnamic acid complex; cinnamic acid can enter into the primary substrate-binding pocket and alter the environment around Trp and Tyr residues.
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Affiliation(s)
- Hongmei Zhang
- Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province 224002, People's Republic of China
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27
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Vogt AD, Pozzi N, Chen Z, Di Cera E. Essential role of conformational selection in ligand binding. Biophys Chem 2013; 186:13-21. [PMID: 24113284 DOI: 10.1016/j.bpc.2013.09.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 11/26/2022]
Abstract
Two competing and mutually exclusive mechanisms of ligand recognition - conformational selection and induced fit - have dominated our interpretation of ligand binding in biological macromolecules for almost six decades. Conformational selection posits the pre-existence of multiple conformations of the macromolecule from which the ligand selects the optimal one. Induced fit, on the other hand, postulates the existence of conformational rearrangements of the original conformation into an optimal one that are induced by binding of the ligand. In the former case, conformational transitions precede the binding event; in the latter, conformational changes follow the binding step. Kineticists have used a facile criterion to distinguish between the two mechanisms based on the dependence of the rate of relaxation to equilibrium, kobs, on the ligand concentration, [L]. A value of kobs decreasing hyperbolically with [L] has been seen as diagnostic of conformational selection, while a value of kobs increasing hyperbolically with [L] has been considered diagnostic of induced fit. However, this simple conclusion is only valid under the rather unrealistic assumption of conformational transitions being much slower than binding and dissociation events. In general, induced fit only produces values of kobs that increase with [L] but conformational selection is more versatile and is associated with values of kobs that increase with, decrease with or are independent of [L]. The richer repertoire of kinetic properties of conformational selection applies to kinetic mechanisms with single or multiple saturable relaxations and explains the behavior of nearly all experimental systems reported in the literature thus far. Conformational selection is always sufficient and often necessary to account for the relaxation kinetics of ligand binding to a biological macromolecule and is therefore an essential component of any binding mechanism. On the other hand, induced fit is never necessary and only sufficient in a few cases. Therefore, the long assumed importance and preponderance of induced fit as a mechanism of ligand binding should be reconsidered.
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Affiliation(s)
- Austin D Vogt
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
| | - Zhiwei Chen
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States.
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28
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Vogt AD, Di Cera E. Conformational selection is a dominant mechanism of ligand binding. Biochemistry 2013; 52:5723-9. [PMID: 23947609 DOI: 10.1021/bi400929b] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular recognition in biological macromolecules is achieved by binding interactions coupled to conformational transitions that precede or follow the binding step, two limiting mechanisms known as conformational selection and induced fit, respectively. Sorting out the contribution of these mechanisms to any binding interaction remains a challenging task of general interest in biochemistry. Here we show that conformational selection is associated with a vast repertoire of kinetic behaviors, can never be disproved a priori as a mechanism of ligand binding, and is sufficient to explain the relaxation kinetics documented experimentally for a large number of systems. On the other hand, induced fit features a narrow spectrum of kinetic behaviors and can be disproved in many cases in which conformational selection offers the only possible explanation. This conclusion offers a paradigm shift in the analysis of relaxation kinetics, with conformational selection acquiring preeminence as a mechanism of ligand binding. The dominant role of conformational selection supports the emerging structural view of the macromolecule as a conformational ensemble from which the ligand selects the initial optimal fit to produce a biological response.
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Affiliation(s)
- Austin D Vogt
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Missouri 63104, United States
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29
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Gaspar ME, Csermely P. Rigidity and flexibility of biological networks. Brief Funct Genomics 2012; 11:443-56. [DOI: 10.1093/bfgp/els023] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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30
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Vogt AD, Di Cera E. Conformational selection or induced fit? A critical appraisal of the kinetic mechanism. Biochemistry 2012; 51:5894-902. [PMID: 22775458 DOI: 10.1021/bi3006913] [Citation(s) in RCA: 229] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For almost five decades, two competing mechanisms of ligand recognition, conformational selection and induced fit, have dominated our interpretation of ligand binding in biological macromolecules. When binding-dissociation events are fast compared to conformational transitions, the rate of approach to equilibrium, k(obs), becomes diagnostic of conformational selection or induced fit based on whether it decreases or increases, respectively, with the ligand concentration, [L]. However, this simple conclusion based on the rapid equilibrium approximation is not valid in general. Here we show that conformational selection is associated with a rich repertoire of kinetic properties, with k(obs) decreasing or increasing with [L] depending on the relative magnitude of the rate of ligand dissociation, k(off), and the rate of conformational isomerization, k(r). We prove that, even for the simplest two-step mechanism of ligand binding, a decrease in k(obs) with [L] is unequivocal evidence of conformational selection, but an increase in k(obs) with [L] is not unequivocal evidence of induced fit. Ligand binding to glucokinase, thrombin, and its precursor prethrombin-2 are used as relevant examples. We conclude that conformational selection as a mechanism for a ligand binding to its target may be far more common than currently believed.
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Affiliation(s)
- Austin D Vogt
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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31
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Pozzi N, Vogt AD, Gohara DW, Di Cera E. Conformational selection in trypsin-like proteases. Curr Opin Struct Biol 2012; 22:421-31. [PMID: 22664096 DOI: 10.1016/j.sbi.2012.05.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 05/08/2012] [Accepted: 05/10/2012] [Indexed: 01/30/2023]
Abstract
For over four decades, two competing mechanisms of ligand recognition--conformational selection and induced-fit--have dominated our interpretation of protein allostery. Defining the mechanism broadens our understanding of the system and impacts our ability to design effective drugs and new therapeutics. Recent kinetics studies demonstrate that trypsin-like proteases exist in equilibrium between two forms: one fully accessible to substrate (E) and the other with the active site occluded (E*). Analysis of the structural database confirms existence of the E* and E forms and vouches for the allosteric nature of the trypsin fold. Allostery in terms of conformational selection establishes an important paradigm in the protease field and enables protein engineers to expand the repertoire of proteases as therapeutics.
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Affiliation(s)
- Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
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32
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Zamyatnin AA, Voronina OL. Food protein fragments are regulatory oligopeptides. BIOCHEMISTRY (MOSCOW) 2012; 77:502-10. [DOI: 10.1134/s0006297912050100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Allostery in trypsin-like proteases suggests new therapeutic strategies. Trends Biotechnol 2011; 29:577-85. [PMID: 21726912 DOI: 10.1016/j.tibtech.2011.06.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/19/2011] [Accepted: 06/02/2011] [Indexed: 11/21/2022]
Abstract
Trypsin-like proteases (TLPs) are a large family of enzymes responsible for digestion, blood coagulation, fibrinolysis, development, fertilization, apoptosis and immunity. A current paradigm posits that the irreversible transition from an inactive zymogen to the active protease form enables productive interaction with substrate and catalysis. Analysis of the entire structural database reveals two distinct conformations of the active site: one fully accessible to substrate (E) and the other occluded by the collapse of a specific segment (E*). The allosteric E*-E equilibrium provides a reversible mechanism for activity and regulation in addition to the irreversible zymogen to protease conversion and points to new therapeutic strategies aimed at inhibiting or activating the enzyme. In this review, we discuss relevant examples, with emphasis on the rational engineering of anticoagulant thrombin mutants.
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Rauscher AÁ, Simon Z, Szöllosi GJ, Gráf L, Derényi I, Malnasi-Csizmadia A. Temperature dependence of internal friction in enzyme reactions. FASEB J 2011; 25:2804-13. [PMID: 21555355 DOI: 10.1096/fj.11-180794] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Our aim was to elucidate the physical background of internal friction of enzyme reactions by investigating the temperature dependence of internal viscosity. By rapid transient kinetic methods, we directly measured the rate constant of trypsin 4 activation, which is an interdomain conformational rearrangement, as a function of temperature and solvent viscosity. We found that the apparent internal viscosity shows an Arrhenius-like temperature dependence, which can be characterized by the activation energy of internal friction. Glycine and alanine mutations were introduced at a single position of the hinge of the interdomain region to evaluate how the flexibility of the hinge affects internal friction. We found that the apparent activation energies of the conformational change and the internal friction are interconvertible parameters depending on the protein flexibility. The more flexible a protein was, the greater proportion of the total activation energy of the reaction was observed as the apparent activation energy of internal friction. Based on the coupling of the internal and external movements of the protein during its conformational change, we constructed a model that quantitatively relates activation energy, internal friction, and protein flexibility.
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Affiliation(s)
- Anna Á Rauscher
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
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Dumez ME, Teller N, Mercier F, Tanaka T, Vandenberghe I, Vandenbranden M, Devreese B, Luxen A, Frère JM, Matagne A, Jacquet A, Galleni M, Chevigné A. Activation mechanism of recombinant Der p 3 allergen zymogen: contribution of cysteine protease Der p 1 and effect of propeptide glycosylation. J Biol Chem 2008; 283:30606-17. [PMID: 18725410 PMCID: PMC2662151 DOI: 10.1074/jbc.m803041200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Revised: 07/18/2008] [Indexed: 11/06/2022] Open
Abstract
The trypsin-like protease Der p 3, a major allergen of the house dust mite Dermatophagoides pteronyssinus, is synthesized as a zymogen, termed proDer p 3. No recombinant source of Der p 3 has been described yet, and the zymogen maturation mechanism remains to be elucidated. The Der p 3 zymogen was produced in Pichia pastoris. We demonstrated that the recombinant zymogen is glycosylated at the level of its propeptide. We showed that the activation mechanism of proDer p 3 is intermolecular and is mediated by the house dust mite cysteine protease Der p 1. The primary structure of the proDer p 3 propeptide is associated with a unique zymogen activation mechanism, which is different from those described for the trypsin-like family and relies on the house dust mite papain-like protease Der p 1. This is the first report of a recombinant source of Der p 3, with the same enzymatic activity as the natural enzyme and trypsin. Glycosylation of the propeptide was found to decrease the rate of maturation. Finally, we showed that recombinant Der p 3 is inhibited by the free modified prosequence T(P1)R.
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Affiliation(s)
- Marie-Eve Dumez
- Centre for Protein Engineering, Centre de Recherches du Cyclotron, Université de Liège, Liège 4000, Belgium
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Toso R, Zhu H, Camire RM. The conformational switch from the factor X zymogen to protease state mediates exosite expression and prothrombinase assembly. J Biol Chem 2008; 283:18627-35. [PMID: 18460471 DOI: 10.1074/jbc.m802205200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Zymogens of the chymotrypsin-like serine protease family are converted to the protease state following insertion of a newly formed, highly conserved N terminus. This transition is accompanied by active site formation and ordering of several surface loops in the catalytic domain. Here we show that disruption of this transition in factor X through mutagenesis (FXa(I16L) and FXa(V17A)) not only alters active site function, but also significantly impairs Na(+) and factor Va binding. Active site binding was improved in the presence of high NaCl or with saturating amounts of factor Va membranes, suggesting that allosteric linkage exists between these sites. In line with this, irreversible stabilization of FXa(I16L) with Glu-Gly-Arg-chloromethyl ketone fully rescued FVa binding. Furthermore, the K(m) for prothrombin conversion with the factor Xa variants assembled into prothrombinase was unaltered, whereas the k(cat) was modestly reduced (3- to 4-fold). These findings show that intramolecular activation of factor X following the zymogen to protease transition not only drives catalytic site activation but also contributes to the formation of the Na(+) and factor Va binding sites. This structural plasticity of the catalytic domain plays a key role in the regulation of exosite expression and prothrombinase assembly.
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Affiliation(s)
- Raffaella Toso
- Department of Pediatrics, Division of Hematology, The Children's Hospital of Philadelphia, Pennsylvania 19104, USA
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