1
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Omar MN, Rahman RNZRA, Noor NDM, Latip W, Knight VF, Ali MSM. Exploring the Antarctic aminopeptidase P from Pseudomonas sp. strain AMS3 through structural analysis and molecular dynamics simulation. J Biomol Struct Dyn 2024:1-13. [PMID: 38555730 DOI: 10.1080/07391102.2024.2331093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
Aminopeptidase P (APPro) is a crucial metalloaminopeptidase involved in amino acid cleavage from peptide N-termini, playing essential roles as versatile biocatalysts with applications ranging from pharmaceuticals to industrial processes. Despite acknowledging its potential for catalysis in lower temperatures, detailed molecular basis and biotechnological implications in cold environments are yet to be explored. Therefore, this research aims to investigate the molecular mechanisms underlying the cold-adapted characteristics of APPro from Pseudomonas sp. strain AMS3 (AMS3-APPro) through a detailed analysis of its structure and dynamics. In this study, structure analysis and molecular dynamics (MD) simulation of a predicted model of AMS3-APPro has been performed at different temperatures to assess structural flexibility and thermostability across a temperature range of 0-60 °C over 100 ns. The MD simulation results revealed that the structure were able to remain stable at low temperatures. Increased temperatures present a potential threat to the overall stability of AMS3-APPro by disrupting the intricate hydrogen bond networks crucial for maintaining structural integrity, thereby increasing the likelihood of protein unfolding. While the metal binding site at the catalytic core exhibits resilience at higher temperatures, highlighting its local structural integrity, the overall enzyme structure undergoes fluctuations and potential denaturation. This extensive structural instability surpasses the localized stability observed at the metal binding site. Consequently, these assessments offer in-depth understanding of the cold-adapted characteristics of AMS3-APPro, highlighting its capability to uphold its native conformation and stability in low-temperature environments. In summary, this research provides valuable insights into the cold-adapted features of AMS3-APPro, suggesting its efficient operation in low thermal conditions, particularly relevant for potential biotechnological applications in cold environments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhamad Nadzmi Omar
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Wahhida Latip
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Victor Feizal Knight
- Research Centre for Chemical Defence, National Defence University of Malaysia, Kem Perdana Sungai Besi, Kuala Lumpur, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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2
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Eni-Aganga I, Lanaghan ZM, Balasubramaniam M, Dash C, Pandhare J. PROLIDASE: A Review from Discovery to its Role in Health and Disease. Front Mol Biosci 2021; 8:723003. [PMID: 34532344 PMCID: PMC8438212 DOI: 10.3389/fmolb.2021.723003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
Prolidase (peptidase D), encoded by the PEPD gene, is a ubiquitously expressed cytosolic metalloproteinase, the only enzyme capable of cleaving imidodipeptides containing C-terminal proline or hydroxyproline. Prolidase catalyzes the rate-limiting step during collagen recycling and is essential in protein metabolism, collagen turnover, and matrix remodeling. Prolidase, therefore plays a crucial role in several physiological processes such as wound healing, inflammation, angiogenesis, cell proliferation, and carcinogenesis. Accordingly, mutations leading to loss of prolidase catalytic activity result in prolidase deficiency a rare autosomal recessive metabolic disorder characterized by defective wound healing. In addition, alterations in prolidase enzyme activity have been documented in numerous pathological conditions, making prolidase a useful biochemical marker to measure disease severity. Furthermore, recent studies underscore the importance of a non-enzymatic role of prolidase in cell regulation and infectious disease. This review aims to provide comprehensive information on prolidase, from its discovery to its role in health and disease, while addressing the current knowledge gaps.
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Affiliation(s)
- Ireti Eni-Aganga
- Center for AIDS Health Disparities Research, Nashville, TN, United States.,School of Graduate Studies and Research, Nashville, TN, United States.,Department of Microbiology, Immunology and Physiology, Nashville, TN, United States
| | - Zeljka Miletic Lanaghan
- Center for AIDS Health Disparities Research, Nashville, TN, United States.,Pharmacology Graduate Program, Vanderbilt University, Nashville, TN, United States
| | - Muthukumar Balasubramaniam
- Center for AIDS Health Disparities Research, Nashville, TN, United States.,Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, TN, United States
| | - Chandravanu Dash
- Center for AIDS Health Disparities Research, Nashville, TN, United States.,School of Graduate Studies and Research, Nashville, TN, United States.,Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, TN, United States
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Nashville, TN, United States.,School of Graduate Studies and Research, Nashville, TN, United States.,Department of Microbiology, Immunology and Physiology, Nashville, TN, United States
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3
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Wilk P, Wątor E, Weiss MS. Prolidase - A protein with many faces. Biochimie 2020; 183:3-12. [PMID: 33045291 DOI: 10.1016/j.biochi.2020.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/31/2020] [Accepted: 09/15/2020] [Indexed: 12/21/2022]
Abstract
Prolidase is a metal-dependent peptidase specialized in the cleavage of dipeptides containing proline or hydroxyproline on their C-termini. Prolidase homologues are found in all kingdoms of life. The importance of prolidase in human health is underlined by a rare hereditary syndrome referred to as Prolidase Deficiency. A growing number of studies highlight the importance of prolidase in various other human conditions, including cancer. Some recent studies link prolidase's activity-independent regulatory role to tumorigenesis. Furthermore, the enzyme or engineered variants have some applications in biotechnology. In this short review, we aim to highlight different aspects of the protein the importance of which is increasingly recognized over the last years.
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Affiliation(s)
- Piotr Wilk
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Elżbieta Wątor
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489, Berlin, Germany
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4
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Winslow JW, Limesand KH, Zhao N. The Functions of ZIP8, ZIP14, and ZnT10 in the Regulation of Systemic Manganese Homeostasis. Int J Mol Sci 2020; 21:ijms21093304. [PMID: 32392784 PMCID: PMC7246657 DOI: 10.3390/ijms21093304] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/27/2022] Open
Abstract
As an essential nutrient, manganese is required for the regulation of numerous cellular processes, including cell growth, neuronal health, immune cell function, and antioxidant defense. However, excess manganese in the body is toxic and produces symptoms of neurological and behavioral defects, clinically known as manganism. Therefore, manganese balance needs to be tightly controlled. In the past eight years, mutations of genes encoding metal transporters ZIP8 (SLC39A8), ZIP14 (SLC39A14), and ZnT10 (SLC30A10) have been identified to cause dysregulated manganese homeostasis in humans, highlighting the critical roles of these genes in manganese metabolism. This review focuses on the most recent advances in the understanding of physiological functions of these three identified manganese transporters and summarizes the molecular mechanisms underlying how the loss of functions in these genes leads to impaired manganese homeostasis and human diseases.
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5
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Nicolafrancesco C, Porcaro F, Pis I, Nappini S, Simonelli L, Marini C, Frangipani E, Visaggio D, Visca P, Mobilio S, Meneghini C, Fratoddi I, Iucci G, Battocchio C. Gallium- and Iron-Pyoverdine Coordination Compounds Investigated by X-ray Photoelectron Spectroscopy and X-ray Absorption Spectroscopy. Inorg Chem 2019; 58:4935-4944. [DOI: 10.1021/acs.inorgchem.8b03574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Chiara Nicolafrancesco
- Department of Science, Roma Tre University, Via della Vasca Navale 79, 00146 Rome, Italy
| | - Francesco Porcaro
- University of Bordeaux, CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Igor Pis
- Elettra-Sincrotrone Trieste S.C.p.A., SS 14, km 163,5 Basovizza, I-34149 Trieste, Italy
| | - Silvia Nappini
- IOM-CNR Laboratorio TASC, SS 14, Km 163,5 Basovizza, I-34149 Trieste, Italy
| | - Laura Simonelli
- CELLS—ALBA Synchrotron Radiation Facility, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Carlo Marini
- CELLS—ALBA Synchrotron Radiation Facility, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - Emanuela Frangipani
- Department of Science, Roma Tre University, Via della Vasca Navale 79, 00146 Rome, Italy
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, 61029 Province of Pesaro and Urbino, Italy
| | - Daniela Visaggio
- Department of Science, Roma Tre University, Via della Vasca Navale 79, 00146 Rome, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, Via della Vasca Navale 79, 00146 Rome, Italy
| | - Settimio Mobilio
- Department of Science, Roma Tre University, Via della Vasca Navale 79, 00146 Rome, Italy
| | - Carlo Meneghini
- Department of Science, Roma Tre University, Via della Vasca Navale 79, 00146 Rome, Italy
| | | | - Giovanna Iucci
- Department of Science, Roma Tre University, Via della Vasca Navale 79, 00146 Rome, Italy
| | - Chiara Battocchio
- Department of Science, Roma Tre University, Via della Vasca Navale 79, 00146 Rome, Italy
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6
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A plasma proteolysis pathway comprising blood coagulation proteases. Oncotarget 2018; 7:40919-40938. [PMID: 27248165 PMCID: PMC5173032 DOI: 10.18632/oncotarget.7261] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 01/29/2016] [Indexed: 01/05/2023] Open
Abstract
Coagulation factors are essential for hemostasis. Here, we show that these factors also team up to degrade plasma proteins that are unrelated to hemostasis. Prolidase, SRC and amyloid β1-42 (Aβ1-42) are used as probes. Each probe, upon entering the blood circulation, binds and activates factor XII (FXII), triggering the intrinsic and common coagulation cascades, which in turn activate factor VII, a component of the extrinsic coagulation cascade. Activated factor VII (FVIIa) rapidly degrades the circulating probes. Therefore, FXII and FVIIa serve as the sensor/initiator and executioner, respectively, for the proteolysis pathway. Moreover, activation of this pathway by one probe leads to the degradation of all three probes. Significant activation of this pathway follows tissue injury and may also occur in other disorders, e.g., Alzheimer's disease, of which Aβ1-42 is a key driver. However, enoxaparin, a clinically used anticoagulant, inhibits the proteolysis pathway and elevates plasma levels of the probes. Enoxaparin may also mitigate potential impact of activators of the proteolysis pathway on coagulation. Our results suggest that the proteolysis pathway is important for maintaining low levels of various plasma proteins. Our finding that enoxaparin inhibits this pathway provides a means to control it. Inhibition of this pathway may facilitate the development of disease biomarkers and protein therapeutics, e.g., plasma Aβ1-42 as a biomarker of Alzheimer's disease or recombinant human prolidase as an antitumor agent.
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7
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Abstract
p53 tumor suppressor responds to various cellular stresses and regulates cell fate. Here, we show that peptidase D (PEPD) binds and suppresses over half of nuclear and cytoplasmic p53 under normal conditions, independent of its enzymatic activity. Eliminating PEPD causes cell death and tumor regression due to p53 activation. PEPD binds to the proline-rich domain in p53, which inhibits phosphorylation of nuclear p53 and MDM2-mediated mitochondrial translocation of nuclear and cytoplasmic p53. However, the PEPD-p53 complex is critical for p53 response to stress, as stress signals doxorubicin and H2O2 each must free p53 from PEPD in order to achieve robust p53 activation, which is mediated by reactive oxygen species. Thus, PEPD stores p53 for the stress response, but this also renders cells dependent on PEPD for survival, as it suppresses p53. This finding provides further understanding of p53 regulation and may have significant implications for the treatment of cancer and other diseases. p53 is a pivotal tumour suppressor that is activated by various cellular stress inducers. Here, the authors show that peptidase D (PEPD) promotes the growth of cancer cells by suppressing p53 and that the complex PEPD-p53 is critical for robust p53 activation in response to stress signals.
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8
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Peng CT, Liu L, Li CC, He LH, Li T, Shen YL, Gao C, Wang NY, Xia Y, Zhu YB, Song YJ, Lei Q, Yu LT, Bao R. Structure-Function Relationship of Aminopeptidase P from Pseudomonas aeruginosa. Front Microbiol 2017; 8:2385. [PMID: 29259588 PMCID: PMC5723419 DOI: 10.3389/fmicb.2017.02385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/20/2017] [Indexed: 02/05/2023] Open
Abstract
PepP is a virulence-associated gene in Pseudomonas aeruginosa, making it an attractive target for anti-P. aeruginosa drug development. The encoded protein, aminopeptidases P (Pa-PepP), is a type of X-prolyl peptidase that possesses diverse biological functions. The crystal structure verified its canonical pita-bread fold and functional tetrameric assembly, and the functional studies measured the influences of different metal ions on the activity. A trimetal manganese cluster was observed at the active site, elucidating the mechanism of inhibition by metal ions. Additionally, a loop extending from the active site appeared to be important for specific large-substrate binding. Based on the structural comparison and bacterial invasion assays, we showed that this non-conserved surface loop was critical for P. aeruginosa virulence. Taken together, these findings can extend our understanding of the catalytic mechanism and virulence-related functions of Pa-PepP and provide a solid foundation for the design of specific inhibitors against pathogenic-bacterial infections.
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Affiliation(s)
- Cui-Ting Peng
- Pharmaceutical and Biological Engineering Department, School of Chemical Engineering, Sichuan University, Chengdu, China,Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Li Liu
- Pharmaceutical and Biological Engineering Department, School of Chemical Engineering, Sichuan University, Chengdu, China,Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Chang-Cheng Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Li-Hui He
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Tao Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ya-Lin Shen
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Chao Gao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ning-Yu Wang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China,School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Yong Xia
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Yi-Bo Zhu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ying-Jie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Qian Lei
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Luo-Ting Yu
- Pharmaceutical and Biological Engineering Department, School of Chemical Engineering, Sichuan University, Chengdu, China,Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China,*Correspondence: Rui Bao, Luo-Ting Yu,
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China,*Correspondence: Rui Bao, Luo-Ting Yu,
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9
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Wilk P, Uehlein M, Kalms J, Dobbek H, Mueller U, Weiss MS. Substrate specificity and reaction mechanism of human prolidase. FEBS J 2017; 284:2870-2885. [DOI: 10.1111/febs.14158] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/23/2017] [Accepted: 06/30/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Piotr Wilk
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
- Institut für Biologie, Strukturbiologie/Biochemie; Humboldt-Universität zu Berlin; Germany
| | - Monika Uehlein
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
| | - Jacqueline Kalms
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie; Humboldt-Universität zu Berlin; Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
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10
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Tereshchenkova VF, Goptar IA, Zhuzhikov DP, Belozersky MA, Dunaevsky YE, Oppert B, Filippova IY, Elpidina EN. Prolidase is a critical enzyme for complete gliadin digestion in Tenebrio molitor larvae. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2017; 95:e21395. [PMID: 28660745 DOI: 10.1002/arch.21395] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Prolidase is a proline-specific metallopeptidase that cleaves imidodipeptides with C-terminal Pro residue. Prolidase was purified and characterized from the Tenebrio molitor larval midgut. The enzyme was localized in the soluble fraction of posterior midgut tissues, corresponding to a predicted cytoplasmic localization of prolidase according to the structure of the mRNA transcript. Expression of genes encoding prolidase and the major digestive proline-specific peptidase (PSP)-dipeptidyl peptidase 4-were similar. The pH optimum of T. molitor prolidase was 7.5, and the enzyme was inhibited by Z-Pro, indicating that it belongs to type I prolidases. In mammals, prolidase is particularly important in the catabolism of a proline-rich protein-collagen. We propose that T. molitor larval prolidase is a critical enzyme for the final stages of digestion of dietary proline-rich gliadins, providing hydrolysis of imidodipeptides in the cytoplasm of midgut epithelial cells. We propose that the products of hydrolysis are absorbed from the luminal contents by peptide transporters, which we have annotated in the T. molitor larval gut transcriptome. The origin of prolidase substrates in the insect midgut is discussed in the context of overall success of grain feeding insects.
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Affiliation(s)
| | - Irina A Goptar
- Chemical Faculty, Lomonosov Moscow State University, Moscow, Russia
| | | | - Mikhail A Belozersky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yakov E Dunaevsky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, KS, USA
| | | | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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11
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Kaleli S, Kotan D, Akdogan M, Ceylan M, Yalcin A. Serum Prolidase Activity as a Biomarker for Choroid Plexus Calcification. TOHOKU J EXP MED 2017; 238:255-9. [PMID: 27000973 DOI: 10.1620/tjem.238.255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The choroid plexus (CP) performs multiple functions such as secretion and reabsorption. CP also acts as the blood-cerebrospinal fluid barrier. Prolidase plays an important role in collagen metabolism by degrading imidodipeptides, in which proline or hydroxyproline residue is located at the C-terminal end. Serum prolidase activity (SPA) may reflect the degree of fibrosis and inflammation. Choroid plexus calcification (CPC) is considered as the physiological calcification of the brain, and CPC is diagnosed by the presence of calcification in the anatomical region on computed tomography (CT). Here, CPC and non-calcified CP were defined by Hounsfield Units (HU) values of > 150 and < 50, respectively. We aimed to measure SPA in subjects with CPC and those with non-calcified CP. This study included 89 subjects who were admitted to the neurology clinic and underwent CT: 44 subjects with CPC and 45 subjects with non-calcified CP. The neurological examination of all subjects was normal; namely, the subjects with CPC were asymptomatic. The SPA level was significantly higher in the CPC group than that in the non-calcified CP group (p < 0.002), and there was a significant positive correlation between vitamin D and SPA levels in the CPC group. In contrast, the vitamin D and parathyroid hormone levels were higher in the CPC group, but the difference was not statically significant (p > 0.05). These findings indicate that SPA is a biomarker for CPC that may be predictive of future brain disease.
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Affiliation(s)
- Suleyman Kaleli
- Department of Medical Biology, Medicine Faculty, Sakarya University
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12
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Tierney DL, Schenk G. X-ray absorption spectroscopy of dinuclear metallohydrolases. Biophys J 2015; 107:1263-72. [PMID: 25229134 DOI: 10.1016/j.bpj.2014.07.066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 06/14/2014] [Accepted: 07/24/2014] [Indexed: 12/26/2022] Open
Abstract
In this mini-review, we briefly discuss the physical origin of x-ray absorption spectroscopy (XAS) before illustrating its application using dinuclear metallohydrolases as exemplary systems. The systems we have selected for illustrative purposes present a challenging problem for XAS, one that is ideal to demonstrate the potential of this methodology for structure/function studies of metalloenzymes in general. When the metal ion is redox active, XAS provides a sensitive measure of oxidation-state-dependent differences. When the metal ion is zinc, XAS is the only spectroscopic method that will provide easily accessible structural information in solution. In the case of heterodimetallic sites, XAS has the unique ability to interrogate each metal site independently in the same sample. One of the strongest advantages of XAS is its ability to examine metal ion site structures with crystallographic precision, without the need for a crystal. This is key for studying flexible metal ion sites, such as those described in the selected examples, because it allows one to monitor structural changes that occur during substrate turnover.
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Affiliation(s)
- David L Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio.
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
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13
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Meneghini C, Leboffe L, Bionducci M, Fanali G, Meli M, Colombo G, Fasano M, Ascenzi P, Mobilio S. The five-to-six-coordination transition of ferric human serum heme-albumin is allosterically-modulated by ibuprofen and warfarin: a combined XAS and MD study. PLoS One 2014; 9:e104231. [PMID: 25153171 PMCID: PMC4143227 DOI: 10.1371/journal.pone.0104231] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/08/2014] [Indexed: 12/20/2022] Open
Abstract
Human serum albumin (HSA) is involved physiologically in heme scavenging; in turn, heme-albumin (HSA-heme-Fe) displays globin-like properties. Here, the allosteric effect of ibuprofen and warfarin on the local atomic structure around the ferric heme-Fe (heme-Fe(III)) atom of HSA-heme-Fe (HSA-heme-Fe(III)) has been probed by Fe-K edge X-ray absorption spectroscopy (XAS). The quantitative analysis of the Fe-K edge extended X-ray absorption fine structure (EXAFS) signals and modeling of the near edge (XANES) spectral features demonstrated that warfarin and ibuprofen binding modify the local structure of the heme-Fe(III). Combined XAS data analysis and targeted molecular dynamics (MD) simulations provided atomic resolution insights of protein structural rearrangements required to accommodate the heme-Fe(III) upon ibuprofen and warfarin binding. In the absence of drugs, the heme-Fe(III) atom is penta-coordinated having distorted 4+1 configuration made by the nitrogen atoms of the porphyrin ring and the oxygen phenoxy atom of the Tyr161 residue. MD simulations show that ibuprofen and warfarin association to the secondary fatty acid (FA) binding site 2 (FA2) induces a reorientation of domain I of HSA-heme-Fe(III), this leads to the redirection of the His146 residue providing an additional bond to the heme-Fe(III) atom, providing the 5+1 configuration. The comparison of Fe-K edge XANES spectra calculated using MD structures with those obtained experimentally confirms the reliability of the proposed structural model. As a whole, combining XAS and MD simulations it has been possible to provide a reliable model of the heme-Fe(III) atom coordination state and to understand the complex allosteric transition occurring in HSA-heme-Fe(III) upon ibuprofen and warfarin binding.
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Affiliation(s)
| | - Loris Leboffe
- Department of Sciences, Roma Tre University, Roma, Italy
- National Institute of Biostructures and Biosystems, Roma, Italy
| | | | - Gabriella Fanali
- Biomedical Research Division, Department of Theoretical and Applied Sciences, and Center of Neuroscience, University of Insubria, Busto Arsizio (VA), Italy
| | - Massimiliano Meli
- Institute for Molecular Recognition Chemistry, National Research Council, Milano, Italy
| | - Giorgio Colombo
- Institute for Molecular Recognition Chemistry, National Research Council, Milano, Italy
| | - Mauro Fasano
- Biomedical Research Division, Department of Theoretical and Applied Sciences, and Center of Neuroscience, University of Insubria, Busto Arsizio (VA), Italy
| | - Paolo Ascenzi
- National Institute of Biostructures and Biosystems, Roma, Italy
- Interdepartmental Laboratory of Electron Microscopy, Roma Tre University, Roma, Italy
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14
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Identification of prolidase as a high affinity ligand of the ErbB2 receptor and its regulation of ErbB2 signaling and cell growth. Cell Death Dis 2014; 5:e1211. [PMID: 24810047 PMCID: PMC4047914 DOI: 10.1038/cddis.2014.187] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 03/26/2014] [Accepted: 03/31/2014] [Indexed: 12/25/2022]
Abstract
ErbB2, an important membrane-bound receptor tyrosine kinase, was discovered nearly 30 years ago, but a natural ligand has never been found previously. ErbB2 is also an important oncogene and anticancer target, and its overexpression in cancer is associated with poor disease prognosis. Here, we report that human prolidase (PEPD) is a high affinity ligand of ErbB2 and binds as a homodimer to subdomain 3 in the extracellular domain of this receptor. In ErbB2-overexpressing cells, both ErbB2 monomers and activated dimers exist. PEPD bound to ErbB2 monomers relatively slowly but caused ErbB2 dimerization, ErbB2 phosphorylation and downstream signaling. In contrast, PEPD bound rapidly to ErbB2 homodimers and rapidly silenced ErbB2 dimer-Src signaling, a key oncogenic pathway of ErbB2, by disrupting the association of Src with ErbB2. PEPD also caused pronounced ErbB2 depletion, resulting from ErbB2 internalization and degradation. Moreover, PEPD strongly inhibited the DNA synthesis, anchorage-independent growth and invasion and migration of cells that overexpressed ErbB2 but had no effect on cells without ErbB2 overexpression. Cells became sensitized to PEPD upon achieving stable ErbB2 overexpression. Thus, the impact of PEPD on ErbB2 is predominantly inhibitory, and PEPD targets cells addicted to ErbB2. PEPD is also a dipeptidase, but its enzymatic function is not involved in ErbB2 modulation. These findings revise our understanding of ErbB2 and PEPD and may be especially important for combating ErbB2-positive cancers.
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15
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Besio R, Gioia R, Cossu F, Monzani E, Nicolis S, Cucca L, Profumo A, Casella L, Tenni R, Bolognesi M, Rossi A, Forlino A. Kinetic and structural evidences on human prolidase pathological mutants suggest strategies for enzyme functional rescue. PLoS One 2013; 8:e58792. [PMID: 23516557 PMCID: PMC3596340 DOI: 10.1371/journal.pone.0058792] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 02/06/2013] [Indexed: 12/17/2022] Open
Abstract
Prolidase is the only human enzyme responsible for the digestion of iminodipeptides containing proline or hydroxyproline at their C-terminal end, being a key player in extracellular matrix remodeling. Prolidase deficiency (PD) is an intractable loss of function disease, characterized by mutations in the prolidase gene. The exact causes of activity impairment in mutant prolidase are still unknown. We generated three recombinant prolidase forms, hRecProl-231delY, hRecProl-E412K and hRecProl-G448R, reproducing three mutations identified in homozygous PD patients. The enzymes showed very low catalytic efficiency, thermal instability and changes in protein conformation. No variation of Mn(II) cofactor affinity was detected for hRecProl-E412K; a compromised ability to bind the cofactor was found in hRecProl-231delY and Mn(II) was totally absent in hRecProl-G448R. Furthermore, local structure perturbations for all three mutants were predicted by in silico analysis. Our biochemical investigation of the three causative alleles identified in perturbed folding/instability, and in consequent partial prolidase degradation, the main reasons for enzyme inactivity. Based on the above considerations we were able to rescue part of the prolidase activity in patients’ fibroblasts through the induction of Heath Shock Proteins expression, hinting at new promising avenues for PD treatment.
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Affiliation(s)
- Roberta Besio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Roberta Gioia
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Federica Cossu
- Department of BioSciences, CNR-IBF and CIMAINA, University of Milano, Milano, Italy
| | - Enrico Monzani
- Department of Chemistry, University of Pavia, Pavia, Italy
| | | | - Lucia Cucca
- Department of Chemistry, University of Pavia, Pavia, Italy
| | | | - Luigi Casella
- Department of Chemistry, University of Pavia, Pavia, Italy
| | - Ruggero Tenni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Martino Bolognesi
- Department of BioSciences, CNR-IBF and CIMAINA, University of Milano, Milano, Italy
| | - Antonio Rossi
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
- * E-mail:
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16
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Besio R, Baratto MC, Gioia R, Monzani E, Nicolis S, Cucca L, Profumo A, Casella L, Basosi R, Tenni R, Rossi A, Forlino A. A Mn(II)–Mn(II) center in human prolidase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:197-204. [DOI: 10.1016/j.bbapap.2012.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 12/20/2022]
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17
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Yang L, Li Y, Ding Y, Choi KS, Kazim AL, Zhang Y. Prolidase directly binds and activates epidermal growth factor receptor and stimulates downstream signaling. J Biol Chem 2012; 288:2365-75. [PMID: 23212918 DOI: 10.1074/jbc.m112.429159] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prolidase, also known as Xaa-Pro dipeptidase or peptidase D (PEPD), is a ubiquitously expressed cytosolic enzyme that hydrolyzes dipeptides with proline or hydroxyproline at the carboxyl terminus. In this article, however, we demonstrate that PEPD directly binds to and activates epidermal growth factor receptor (EGFR), leading to stimulation of signaling proteins downstream of EGFR, and that such activity is neither cell-specific nor dependent on the enzymatic activity of PEPD. In line with the pro-survival and pro-proliferation activities of EGFR, PEPD stimulates DNA synthesis. We further show that PEPD activates EGFR only when it is present in the extracellular space, but that PEPD is released from injured cells and tissues and that such release appears to result in EGFR activation. PEPD differs from all known EGFR ligands in that it does not possess an epidermal growth factor (EGF) motif and is not synthesized as a transmembrane precursor, but PEPD binding to EGFR can be blocked by EGF. In conclusion, PEPD is a ligand of EGFR and presents a novel mechanism of EGFR activation.
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Affiliation(s)
- Lu Yang
- Department of Chemoprevention, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
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18
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Kitchener RL, Grunden AM. Prolidase function in proline metabolism and its medical and biotechnological applications. J Appl Microbiol 2012; 113:233-47. [PMID: 22512465 DOI: 10.1111/j.1365-2672.2012.05310.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Prolidase is a multifunctional enzyme that possesses the unique ability to degrade imidodipeptides in which a proline or hydroxyproline residue is located at the C-terminal end. Prolidases have been isolated from archaea and bacteria, where they are thought to participate in proline recycling. In mammalian species, prolidases are found in the cytoplasm and function primarily to liberate proline in the final stage of protein catabolism, particularly during the biosynthesis and degradation of collagen. Collagen comprises nearly one-third of the total protein in the body, and it is essential in maintaining tissue structure and integrity. Prolidase deficiency (PD), a rare autosomal recessive disorder in which mutations in the PEPD gene affect prolidase functionality, tends to have serious and sometimes life-threatening clinical symptoms. Recombinant prolidases have many applications and have been investigated not only as a possible treatment for PD, but also as a part of anti-cancer strategies, a component of biodecontamination cocktails and in the dairy industry. This review will serve to discuss the many in vivo functions of procaryotic and eucaryotic prolidases, as well as the most recent advances in therapeutic and biotechnological application of prolidases.
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Affiliation(s)
- R L Kitchener
- Department of Microbiology, North Carolina State University, Raleigh, NC, USA
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19
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Costante M, Biggemann L, Alamneh Y, Soojhawon I, Short R, Nigam S, Garcia G, Doctor BP, Valiyaveettil M, Nambiar MP. Hydrolysis potential of recombinant human skin and kidney prolidase against diisopropylfluorophosphate and sarin by in vitro analysis. Toxicol In Vitro 2012; 26:182-8. [DOI: 10.1016/j.tiv.2011.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 11/09/2011] [Accepted: 11/10/2011] [Indexed: 11/15/2022]
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20
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Partial Rescue of Biochemical Parameters After Hematopoietic Stem Cell Transplantation in a Patient with Prolidase Deficiency Due to Two Novel PEPD Mutations. JIMD Rep 2011. [PMID: 23430876 DOI: 10.1007/8904_2011_62] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2023] Open
Abstract
Prolidase deficiency (PD) is a rare recessive disorder resulting from mutations in the prolidase gene (PEPD); only 17 causative mutant alleles had been so far characterized. Prolidase is a ubiquitous enzyme that hydrolyses dipeptides with C-terminal proline or hydroxyproline residues and indeed, lack of this enzyme activity causes massive urine excretion of undigested iminodipeptides. The clinical manifestations of PD are widely variable, and include intractable skin ulcers, unusual face, different degree of mental retardation, and recurrent infections. No definitive treatment is at present available.We report an 8-year girl with a typical PD facies, normal intelligence, and recurrent deep ulcerations complicated by infections. She was found to be compound heterozygous for two novel mutations in PEPD, c.1133delACG and c.1301delT, affecting the C-terminal end of the enzyme where the active site is located. Given her life-threatening course, she underwent allogeneic hematopoietic stem cell transplantation (HSCT) from her HLA-identical brother, confirmed heterozygous for the c.1133delACG allele. Successful engraftment was documented by full-donor chimerism. Posttransplant monitoring of erythrocyte prolidase activity showed that the child had converted to a heterozygous pattern. Reduction of excreted urine dipeptides, evaluated by capillary electrophoresis, supported the effectiveness of the treatment. Unfortunately the patient died on day +92 of invasive fungal infection.Despite the unfavorable outcome, we provide the first evidence that HSCT has the potential to reverse some of the biochemical features of PD patients. The indication to transplant must be balanced against the clinical manifestation of individual patients.
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21
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Besio R, Monzani E, Gioia R, Nicolis S, Rossi A, Casella L, Forlino A. Improved prolidase activity assay allowed enzyme kinetic characterization and faster prolidase deficiency diagnosis. Clin Chim Acta 2011; 412:1814-20. [PMID: 21699887 DOI: 10.1016/j.cca.2011.06.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 06/06/2011] [Accepted: 06/08/2011] [Indexed: 11/18/2022]
Abstract
BACKGROUND Prolidase is a metallo-exopeptidase hydrolyzing X-Pro and X-Hyp dipeptides. Its absence or reduced level is typical in prolidase deficiency (PD) patients, and altered prolidase activity was reported in various diseases. Therefore, standardized and accurate measurement of prolidase activity is essential for PD diagnosis, as well as to elucidate the pathophysiology of other disorders. METHODS Human recombinant prolidase was used to optimize a spectrophotometric enzyme activity assay. Kinetic parameters and Mn(2+) affinity were evaluated. The method was validated on blood and fibroblasts from PD patients. RESULTS An activation step consisting in prolidase incubation with 1 mmol/l MnCl(2) and 0.75 mmol/l reduced glutathione at 50°C for 20 min was necessary to obtain the maximum activity and to accurately determine, for the recombinant enzyme, V(max) (489 U/mg), K(m) (5.4 mM) and Mn(2+) affinity (54 mM(-1)). The method applied to PD diagnosis revealed an intra-assay CV=8% for blood and 9% for fibroblasts lysates. The inter-assay CV was 21% for blood and 20% for cell lysates. CONCLUSION We optimized a faster spectrophotometric method to measure the activity when the enzyme is fully activated, this is crucial to allow a reliable evaluation of prolidase activity from different sources.
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Affiliation(s)
- Roberta Besio
- Department of Biochemistry, University of Pavia, Italy
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22
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Jung S, Silvius D, Nolan KA, Borchert GL, Millet YH, Phang JM, Gunn TM. Developmental cardiac hypertrophy in a mouse model of prolidase deficiency. ACTA ACUST UNITED AC 2011; 91:204-17. [DOI: 10.1002/bdra.20789] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 01/11/2011] [Accepted: 01/13/2011] [Indexed: 11/09/2022]
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23
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Alberto ME, Leopoldini M, Russo N. Can Human Prolidase Enzyme Use Different Metals for Full Catalytic Activity? Inorg Chem 2011; 50:3394-403. [DOI: 10.1021/ic1022517] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marta E. Alberto
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Monica Leopoldini
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
| | - Nino Russo
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Universita' della Calabria, I-87030 Arcavacata di Rende (CS), Italy
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