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Doharey PK, Verma P, Dubey A, Singh SK, Kumar M, Tripathi T, Alonazi M, Siddiqi NJ, Sharma B. Biophysical and in-silico studies on the structure-function relationship of Brugia malayi protein disulfide isomerase. J Biomol Struct Dyn 2024; 42:1533-1543. [PMID: 37079006 DOI: 10.1080/07391102.2023.2201849] [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: 11/14/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023]
Abstract
Human Lymphatic filariasis is caused by parasitic nematodes Wuchereria bancrofti, Brugia malayi, and Brugia timori. Protein disulfide isomerase (PDI), a redox-active enzyme, helps to form and isomerize the disulfide bonds, thereby acting as a chaperone. Such activity is essential for activating many essential enzymes and functional proteins. Brugia malayi protein disulfide isomerase (BmPDI) is crucial for parasite survival and an important drug target. Here, we used a combination of spectroscopic and computational analysis to study the structural and functional changes in the BmPDI during unfolding. Tryptophan fluorescence data revealed two well-separated transitions during the unfolding process, suggesting that the unfolding of the BmPDI is non-cooperative. The binding of the fluorescence probe 8-anilino-1-naphthalene sulfonic acid dye (ANS) validated the results obtained by the pH unfolding. The dynamics of molecular simulation performed at different pH conditions revealed the structural basis of BmPDI unfolding. Detailed analysis suggested that under different pH, both the global structure and the conformational dynamics of the active site residues were differentially altered. Our multiparametric study reveals the differential dynamics and collective motions of BmPDI unfolding, providing insights into its structure-function relationship.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Pravesh Verma
- Biochemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Amit Dubey
- Computational Chemistry and Drug discovery Division, Quanta calculus Pvt. Ltd, Kushinagar, India
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Sudhir Kumar Singh
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Manish Kumar
- Department of Biochemistry, University of Allahabad, Allahabad, India
| | - Timir Tripathi
- Department of Biochemistry, North-Eastern Hill University, Umshing, India
| | - Mona Alonazi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nikhat Jamal Siddiqi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Bechan Sharma
- Department of Biochemistry, University of Allahabad, Allahabad, India
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Sinha K, Rule GS. Conformational diversity defines substrate specificity of thymidylate/uridylate kinase from Candida albicans. Proteins 2021; 89:937-944. [PMID: 33682244 DOI: 10.1002/prot.26071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 01/06/2021] [Accepted: 03/04/2021] [Indexed: 11/07/2022]
Abstract
Thymidylate kinase (TMK) from Candida albicans (CaTMK) contains a unique 15 residue insert, the CaLoop, that is not found on other TMKs. CaTMK is proficient at phosphorylating deoxyuridine monophosphate (dUMP), showing a rate 6-fold higher than TMP. It has been shown that deletion of the CaLoop reduces the activity towards dUMP by 19-fold, but has only a modest 4-fold decrease in activity towards TMP. The molecular dynamics calculations presented here show that the increased activity towards dUMP is due to an increase in flexibility and correlated motions of the protein that allows the enzyme-dUMP complex to more readily approach a catalytically competent state. Deletion of the CaLoop allows the dUMP-enzyme complex to adopt catalytically non-functional conformations. In contrast, TMP stabilizes the deletion such that it remains in a functional conformation that is similar to the conformation of the original enzyme.
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Affiliation(s)
- Kaustubh Sinha
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Gordon S Rule
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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Sharma R, Pielstick BA, Bell KA, Nieman TB, Stubbs OA, Yeates EL, Baltrus DA, Grose JH. A Novel, Highly Related Jumbo Family of Bacteriophages That Were Isolated Against Erwinia. Front Microbiol 2019; 10:1533. [PMID: 31428059 PMCID: PMC6690015 DOI: 10.3389/fmicb.2019.01533] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 01/17/2023] Open
Abstract
Erwinia amylovora is a plant pathogen from the Erwiniaceae family and a causative agent of the devastating agricultural disease fire blight. Here we characterize eight lytic bacteriophages of E. amylovora that we isolated from the Wasatch front (Utah, United States) that are highly similar to vB_EamM_Ea35-70 which was isolated in Ontario, Canada. With the genome size ranging from 271 to 275 kb, this is a novel jumbo family of bacteriophages. These jumbo bacteriophages were further characterized through genomic and proteomic comparison, mass spectrometry, host range and burst size. Their proteomes are highly unstudied, with over 200 putative proteins with no known homologs. The production of 27 of these putative proteins was confirmed by mass spectrometry analysis. These bacteriophages appear to be most similar to bacteriophages that infect Pseudomonas and Ralstonia rather than Enterobacteriales bacteria by protein similarity, however, we were only able to detect infection of Erwinia and the closely related strains of Pantoea.
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Affiliation(s)
- Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Brittany A. Pielstick
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Kimberly A. Bell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Tanner B. Nieman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Olivia A. Stubbs
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Edward L. Yeates
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - David A. Baltrus
- School of Plant Sciences, The University of Arizona, Tucson, AZ, United States
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
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Verma P, Doharey PK, Yadav S, Omer A, Singh P, Saxena JK. Molecular cloning and characterization of protein disulfide isomerase of Brugia malayi, a human lymphatic filarial parasite. EXCLI JOURNAL 2017; 16:824-839. [PMID: 28827998 PMCID: PMC5547380 DOI: 10.17179/excli2017-214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/11/2017] [Indexed: 11/29/2022]
Abstract
Lymphatic filariasis results in an altered lymphatic system and the abnormal enlargement of body parts, causing pain, serious disability and social stigma. Effective vaccines are still not available nowadays, drugs against the disease is required. Protein disulfide isomerase (PDI) is an essential catalyst of the endoplasmic reticulum which is involved in folding and chaperone activities in different biological systems. Here, we report the enzymatic characterization of a Brugia malayi Protein disulfide isomerase (BmPDI), which was expressed and purified from Escherichia coli BL21 (DE3). Western blotting analysis showed the recombinant BmPDI could be recognized by anti-BmPDI Rabbit serum. The rBmPDI exhibited an optimum activity at pH 8 and 40 °C. The enzyme was inhibited by aurin and PDI inhibitor. Recombinant BmPDI showed interaction with recombinant Brugia malayi calreticulin (rBmCRT). The three-dimensional model for BmPDI and BmCRT was generated by homology modelling. A total of 25 hydrogen bonds were found to be formed between two interfaces. There are 259 non-bonded contacts present in the BmPDI-BmCRT complex and 12 salt bridges were formed in the interaction.
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Affiliation(s)
- Pravesh Verma
- Division of Biochemistry, CSIR-Central Drug Research Institute, BS10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Pawan Kumar Doharey
- Division of Biochemistry, CSIR-Central Drug Research Institute, BS10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Sunita Yadav
- Division of Biochemistry, CSIR-Central Drug Research Institute, BS10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Ankur Omer
- Division of Toxicology, CSIR-Central Drug Research Institute, BS10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Poonam Singh
- Division of Toxicology, CSIR-Central Drug Research Institute, BS10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Jitendra Kumar Saxena
- Division of Biochemistry, CSIR-Central Drug Research Institute, BS10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
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