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Lu D, Wang W, Li X, Wang L, Guo Y, Zhu C, Wang X, Lian B, Bai J, Zhang Q. Identification and characterization of a PL35 GAGs lyase with 4-O-sulfated N-acetylgalactosamine (A-type)-rich structures producing property. Int J Biol Macromol 2024; 266:131283. [PMID: 38561119 DOI: 10.1016/j.ijbiomac.2024.131283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/18/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Glycosaminoglycan (GAG) lyases are important tools for investigating the structure of GAGs and preparing low-molecular-weight GAGs. The PL35 family, a recently established polysaccharide lyase family, should be further investigated. In this study, we discovered a new GAG lyase, CHa1, which belongs to the PL35 family. When expressed heterologously in Escherichia coli (BL21), CHa1 exhibited high expression levels and solubility. The optimal activity was observed in Tris-HCl buffer (pH 7.0) or sodium phosphate buffer (pH 8.0) at 30 °C. The specific activities towards HA, CSA, CSC, CSD, CSE, and HS were 3.81, 13.03, 36.47, 18.46, 6.46, and 0.50 U/mg protein, respectively. CHa1 digests substrate chains randomly that acting as an endolytic lyase and shows a significant preference for GlcA-containing structures, prefers larger oligosaccharides (≥UDP8) and can generate a series of oligosaccharides composed mainly of the A unit when digesting CSA. These oligosaccharides include ΔC-A, ΔC-A-A, ΔC-A-A-A, ΔC-A-A-A-A, and ΔC-A-A-A-A-A. The residues Tyr257 and His421 play crucial roles in the catalytic process, and Ser211, Asn212, Asn213, Trp214, Gln216, Lys360, Arg460 and Gln462 may participate in the binding process of CHa1. This study on CHa1 contributes to our understanding of the PL35 family and provides valuable tools for investigating the structure of GAGs.
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Affiliation(s)
- Danrong Lu
- School of Life Science and Technology, Shandong Second Medical University, 7166 Baotong West Street, Weifang 261053, China
| | - Wenwen Wang
- School of Life Science and Technology, Shandong Second Medical University, 7166 Baotong West Street, Weifang 261053, China
| | - Xiaoyun Li
- School of Life Science and Technology, Shandong Second Medical University, 7166 Baotong West Street, Weifang 261053, China
| | - Luping Wang
- School of Life Science and Technology, Shandong Second Medical University, 7166 Baotong West Street, Weifang 261053, China
| | - Yankai Guo
- School of Life Science and Technology, Shandong Second Medical University, 7166 Baotong West Street, Weifang 261053, China
| | - Changjian Zhu
- School of Life Science and Technology, Shandong Second Medical University, 7166 Baotong West Street, Weifang 261053, China
| | - Xiaohui Wang
- School of Life Science and Technology, Shandong Second Medical University, 7166 Baotong West Street, Weifang 261053, China
| | - Bo Lian
- School of Life Science and Technology, Shandong Second Medical University, 7166 Baotong West Street, Weifang 261053, China
| | - Jingkun Bai
- School of Life Science and Technology, Shandong Second Medical University, 7166 Baotong West Street, Weifang 261053, China.
| | - Qingdong Zhang
- School of Life Science and Technology, Shandong Second Medical University, 7166 Baotong West Street, Weifang 261053, China.
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Lu D, Wang L, Ning Z, Li Z, Li M, Jia Y, Zhang Q. Identification and characterization of a novel heparinase PCHepII from marine bacterium Puteibacter caeruleilacunae. Sci Rep 2023; 13:20112. [PMID: 37978313 PMCID: PMC10656541 DOI: 10.1038/s41598-023-47493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
Heparin (HP) and heparan sulfate (HS) are multifunctional polysaccharides widely used in clinical therapy. Heparinases (Hepases) are enzymes that specifically catalyse HP and HS degradation, and they are valuable tools for studying the structure and function of these polysaccharides and for preparing low molecular weight heparins. In this study, by searching the NCBI database, a novel enzyme named PCHepII was discovered in the genome of the marine bacterium Puteibacter caeruleilacuae. Heterologously expressed PCHepII in Escherichia coli (BL21) has high expression levels and good solubility, active in sodium phosphate buffer (pH 7.0) at 20°C. PCHepII exhibits an enzyme activity of 254 mU/mg towards HP and shows weak degradation capacity for HS. More importantly, PCHepII prefers to catalyse the high-sulfated regions of HP and HS rather than the low-sulfated regions. Although PCHepII functions primarily as an endolytic Hepase, it mainly generates disaccharide products during the degradation of HP substrates over time. Investigations reveal that PCHepII exhibits a preference for catalysing the degradation of small substrates, especially HP tetrasaccharides. The catalytic sites of PCHepII include the residues His199, Tyr254, and His403, which play crucial roles in the catalytic process. The study and characterization of PCHepII can potentially benefit research and applications involving HP/HS, making it a promising enzyme.
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Affiliation(s)
- Danrong Lu
- School of Life Science and Technology, Weifang Medical University, 7166 Baotong West Street, Weifang, 261053, China
| | - Luping Wang
- School of Life Science and Technology, Weifang Medical University, 7166 Baotong West Street, Weifang, 261053, China
| | - Zeting Ning
- School of Life Science and Technology, Weifang Medical University, 7166 Baotong West Street, Weifang, 261053, China
| | - Zuhui Li
- School of Life Science and Technology, Weifang Medical University, 7166 Baotong West Street, Weifang, 261053, China
| | - Meihua Li
- School of Life Science and Technology, Weifang Medical University, 7166 Baotong West Street, Weifang, 261053, China
| | - Yan Jia
- School of Life Science and Technology, Weifang Medical University, 7166 Baotong West Street, Weifang, 261053, China
| | - Qingdong Zhang
- School of Life Science and Technology, Weifang Medical University, 7166 Baotong West Street, Weifang, 261053, China.
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Chen TT, Lv JJ, Chen L, Li M, Liu LP. Heparanase inhibition leads to improvement in patients with acute gastrointestinal injuries induced by sepsis. World J Gastroenterol 2023; 29:5154-5165. [PMID: 37744293 PMCID: PMC10514756 DOI: 10.3748/wjg.v29.i35.5154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/23/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Patients with sepsis are at high risk for acute gastrointestinal injury (AGI), but the diagnosis and treatment of AGI due to sepsis are unsatisfactory. Heparanase (HPA) plays an important role in septic AGI (S-AGI), but its specific mechanism is not completely understood, and few clinical reports are available. AIM To explore the effect and mechanism of HPA inhibition in S-AGI patients. METHODS In our prospective clinical trial, 48 patients with S-AGI were randomly assigned to a control group to receive conventional treatment, whereas 47 patients were randomly assigned to an intervention group to receive conventional treatment combined with low molecular weight heparin. AGI grade, sequential organ failure assessment score, acute physiology and chronic health evaluation II score, D-dimer, activated partial thromboplastin time (APTT), anti-Xa factor, interleukin-6, tumour necrosis factor-α, HPA, syndecan-1 (SDC-1), LC3B (autophagy marker), intestinal fatty acid binding protein, D-lactate, motilin, gastrin, CD4/CD8, length of intensive care unit (ICU) stay, length of hospital stay and 28-d survival on the 1st, 3rd and 7th d after treatment were compared. Correlations between HPA and AGI grading as well as LC3B were compared. Receiver operator characteristic (ROC) curves were generated to evaluate the diagnostic value of HPA, intestinal fatty acid binding protein and D-lactate in S-AGI. RESULTS Serum HPA and SCD-1 levels were significantly reduced in the intervention group compared with the control group (P < 0.05). In addition, intestinal fatty acid-binding protein, D-lactate, AGI grade, motilin, and gastrin levels and sequential organ failure assessment score were significantly decreased (P < 0.05) in the intervention group. However, LC3B, APTT, anti-Xa factor, and CD4/CD8 were significantly increased (P < 0.05) in the intervention group. No significant differences in interleukin-6, tumour necrosis factor-α, d-dimer, acute physiology and chronic health evaluation II score, length of ICU stay, length of hospital stay, or 28-d survival were noted between the two groups (P > 0.05). Correlation analysis revealed a significant negative correlation between HPA and LC3B and a significant positive correlation between HPA and AGI grade. ROC curve analysis showed that HPA had higher specificity and sensitivity in diagnosis of S-AGI. CONCLUSION HPA has great potential as a diagnostic marker for S-AGI. Inhibition of HPA activity reduces SDC-1 shedding and alleviates S-AGI symptoms. The inhibitory effect of HPA in gastrointestinal protection may be achieved by enhanced autophagy.
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Affiliation(s)
- Ting-Ting Chen
- The First Clinical Medical School of Lanzhou University, Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Jia-Jun Lv
- The First Clinical Medical School of Lanzhou University, Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Ling Chen
- Department of Emergency Critical Care Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Min Li
- Department of Emergency Critical Care Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Li-Ping Liu
- Department of Emergency Critical Care Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
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Chen TT, Lv JJ, Chen L, Gao YW, Liu LP. Role of heparinase in the gastrointestinal dysfunction of sepsis (Review). Exp Ther Med 2022; 23:119. [PMID: 34970342 PMCID: PMC8713170 DOI: 10.3892/etm.2021.11042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
Heparinase (HPA) is a β-D glucuronidase that belongs to the endoglycosidase enzyme family, and plays an important role in numerous pathological and physiological processes, including inflammation, angiogenesis and tumor metastasis. When the expression of HPA is abnormally high, the side chain of heparin sulfate proteoglycans degrades, destroying the cell barrier and leading to the occurrence and development of inflammation, with systemic inflammation occurring in severe cases. Sepsis is a major cause of mortality in critically ill patients. In sepsis, the gastrointestinal tract is the first and most frequently involved target organ, which often leads to gastrointestinal dysfunction. HPA overexpression has been determined to accelerate sepsis progression and gastrointestinal dysfunction; thus, it was hypothesized that HPA may play an important role and may serve as an index for the diagnosis of gastrointestinal dysfunction in sepsis. HPA inhibitors may therefore become applicable as targeted drugs for the treatment of gastrointestinal dysfunction in patients with sepsis. The present review mainly discussed the role of HPA in gastrointestinal dysfunction of sepsis.
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Affiliation(s)
- Ting-Ting Chen
- The First Clinical Medical School of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Jia-Jun Lv
- The First Clinical Medical School of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Ling Chen
- Department of Emergency Critical Care Medicine, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China.,Department of Emergency, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Yu-Wei Gao
- Department of Emergency Critical Care Medicine, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China.,Department of Emergency, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Li-Ping Liu
- Department of Emergency Critical Care Medicine, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China.,Department of Emergency, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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Fluorescence detection of protamine, heparin and heparinase II based on a novel AIE molecule with four carboxyl. Int J Biol Macromol 2020; 156:1153-1159. [PMID: 31756489 DOI: 10.1016/j.ijbiomac.2019.11.150] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 11/23/2022]
Abstract
In this research, a new DSA (Distyryl-anthracene) derivative with four carboxyl groups was designed and synthesized. This molecule exhibits aggregation-induced emission property (AIE). With the AIE character, a convenient and sensitive fluorescent probe for the detection of protamine, heparin and heparinase has been developed. The protamine can directly induce the aggregation of probe, which caused by electrostatic attraction. In this way, the turn-on detection of protamine is achieved, and the detection limit is as low as 30 ng mL-1. When heparin appears, the probes will be redisperse in solution, which causes a decrease in fluorescence intensity. Besides, this method also shows good selectivity and sensitivity, and the linear range of heparin is from 0.08 to 8 μg mL-1 with detection limit of 37 ng mL-1. After hydrolyzing heparin by heparinase, the probes rebind with protamine and the fluorescence enhance. The fluorescence enhancement was linearly related to the concentration of heparinase in the range of 0.02-2.0 μg mL-1 and detection limit as low as 143.7 ng mL-1. In addition, the results exhibited that the recovery percentage of heparinase in bovine samples reached to 96-101%.
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Soares PA, Queiroz IN, Pomin VH. NMR structural biology of sulfated glycans. J Biomol Struct Dyn 2016; 35:1069-1084. [DOI: 10.1080/07391102.2016.1171165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Paulo A.G. Soares
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro , Rio de Janeiro, RJ 21941-913, Brazil
| | - Ismael N.L. Queiroz
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro , Rio de Janeiro, RJ 21941-913, Brazil
| | - Vitor H. Pomin
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro , Rio de Janeiro, RJ 21941-913, Brazil
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Pai PP, Mondal S. MOWGLI: prediction of protein-MannOse interacting residues With ensemble classifiers usinG evoLutionary Information. J Biomol Struct Dyn 2015; 34:2069-83. [PMID: 26457920 DOI: 10.1080/07391102.2015.1106978] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Proteins interact with carbohydrates to perform various cellular interactions. Of the many carbohydrate ligands that proteins bind with, mannose constitute an important class, playing important roles in host defense mechanisms. Accurate identification of mannose-interacting residues (MIR) may provide important clues to decipher the underlying mechanisms of protein-mannose interactions during infections. This study proposes an approach using an ensemble of base classifiers for prediction of MIR using their evolutionary information in the form of position-specific scoring matrix. The base classifiers are random forests trained by different subsets of training data set Dset128 using 10-fold cross-validation. The optimized ensemble of base classifiers, MOWGLI, is then used to predict MIR on protein chains of the test data set Dtestset29 which showed a promising performance with 92.0% accurate prediction. An overall improvement of 26.6% in precision was observed upon comparison with the state-of-art. It is hoped that this approach, yielding enhanced predictions, could be eventually used for applications in drug design and vaccine development.
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Affiliation(s)
- Priyadarshini P Pai
- a Department of Biological Sciences , Birla Institute of Technology and Science-Pilani , K.K. Birla Goa Campus, Near NH17 Bypass Road, Zuarinagar , Goa 403726 , India
| | - Sukanta Mondal
- a Department of Biological Sciences , Birla Institute of Technology and Science-Pilani , K.K. Birla Goa Campus, Near NH17 Bypass Road, Zuarinagar , Goa 403726 , India
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The Calcium Goes Meow: Effects of Ions and Glycosylation on Fel d 1, the Major Cat Allergen. PLoS One 2015. [PMID: 26134118 DOI: 10.1371/journal.pone.0132311.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The major cat allergen, Fel d 1, is a structurally complex protein with two N-glycosylation sites that may be filled by different glycoforms. In addition, the protein contains three putative Ca2+ binding sites. Since the impact of these Fel d 1 structure modifications on the protein dynamics, physiology and pathology are not well established, the present work employed computational biology techniques to tackle these issues. While conformational effects brought upon by glycosylation were identified, potentially involved in cavity volume regulation, our results indicate that only the central Ca2+ ion remains coordinated to Fel d 1 in biological solutions, impairing its proposed role in modulating phospholipase A2 activity. As these results increase our understanding of Fel d 1 structural biology, they may offer new support for understanding its physiological role and impact into cat-promoted allergy.
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Ligabue-Braun R, Sachett LG, Pol-Fachin L, Verli H. The Calcium Goes Meow: Effects of Ions and Glycosylation on Fel d 1, the Major Cat Allergen. PLoS One 2015; 10:e0132311. [PMID: 26134118 PMCID: PMC4489793 DOI: 10.1371/journal.pone.0132311] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 06/11/2015] [Indexed: 12/20/2022] Open
Abstract
The major cat allergen, Fel d 1, is a structurally complex protein with two N-glycosylation sites that may be filled by different glycoforms. In addition, the protein contains three putative Ca2+ binding sites. Since the impact of these Fel d 1 structure modifications on the protein dynamics, physiology and pathology are not well established, the present work employed computational biology techniques to tackle these issues. While conformational effects brought upon by glycosylation were identified, potentially involved in cavity volume regulation, our results indicate that only the central Ca2+ ion remains coordinated to Fel d 1 in biological solutions, impairing its proposed role in modulating phospholipase A2 activity. As these results increase our understanding of Fel d 1 structural biology, they may offer new support for understanding its physiological role and impact into cat-promoted allergy.
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Affiliation(s)
- Rodrigo Ligabue-Braun
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Liana Guimarães Sachett
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Laércio Pol-Fachin
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Hugo Verli
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- * E-mail:
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Identifying Similar Patterns of Structural Flexibility in Proteins by Disorder Prediction and Dynamic Programming. Int J Mol Sci 2015; 16:13829-49. [PMID: 26086829 PMCID: PMC4490526 DOI: 10.3390/ijms160613829] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 12/31/2022] Open
Abstract
Computational methods are prevailing in identifying protein intrinsic disorder. The results from predictors are often given as per-residue disorder scores. The scores describe the disorder propensity of amino acids of a protein and can be further represented as a disorder curve. Many proteins share similar patterns in their disorder curves. The similar patterns are often associated with similar functions and evolutionary origins. Therefore, finding and characterizing specific patterns of disorder curves provides a unique and attractive perspective of studying the function of intrinsically disordered proteins. In this study, we developed a new computational tool named IDalign using dynamic programming. This tool is able to identify similar patterns among disorder curves, as well as to present the distribution of intrinsic disorder in query proteins. The disorder-based information generated by IDalign is significantly different from the information retrieved from classical sequence alignments. This tool can also be used to infer functions of disordered regions and disordered proteins. The web server of IDalign is available at (http://labs.cas.usf.edu/bioinfo/service.html).
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