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Rastogi N, Zarin S, Alam A, Konduru GV, Manjunath P, Mishra A, Kumar S, Nagarajaram HA, Hasnain SE, Ehtesham NZ. Structural and Biophysical properties of therapeutically important proteins Rv1509 and Rv2231A of Mycobacterium tuberculosis. Int J Biol Macromol 2023; 245:125455. [PMID: 37331537 DOI: 10.1016/j.ijbiomac.2023.125455] [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: 04/14/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
Through comparative analyses using BLASTp and BLASTn of the 25 target sequences, our research identified two unique post-transcriptional modifiers, Rv1509 and Rv2231A, which serve as distinctive and characteristic proteins of M.tb - the Signature Proteins. Here, we have characterized these two signature proteins associated with pathophysiology of M.tb which may prove to be therapeutically important targets. Dynamic Light Scattering and Analytical Gel Filtration Chromatography exhibited that Rv1509 exists as a monomer while Rv2231A as a dimer in solution. Secondary structures were determined using Circular Dichroism and further validated through Fourier Transform Infrared spectroscopy. Both the proteins are capable of withstanding a wide range of temperature and pH variations. Fluorescence spectroscopy based binding affinity experiments showed that Rv1509 binds to iron and may promote organism growth by chelating iron. In the case of Rv2231A, a high affinity for its substrate RNA was observed, which is facilitated in presence of Mg2+ suggesting it might have RNAse activity, supporting the prediction through in-silico studies. This is the first study on biophysical characterization of these two therapeutically important proteins, Rv1509 and Rv2231A, providing important insights into their structure -function correlations which are crucial for development of new drugs/ early diagnostics tools targeting these proteins.
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Affiliation(s)
- Nilisha Rastogi
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi 110029, India
| | - Sheeba Zarin
- Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, India; Department of Life Science, School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310, India
| | - Anwar Alam
- Department of Biotechnology, School of Engineering Sciences and Technology, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310, India
| | - Guruprasad Varma Konduru
- Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, India; Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - P Manjunath
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi 110029, India
| | - Abhay Mishra
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Saroj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Hampapathalu Adimurthy Nagarajaram
- Laboratory of Computational Biology, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Prof C.R. Rao Road, Hyderabad 500007, India
| | - Seyed Ehtesham Hasnain
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310, India; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India.
| | - Nasreen Zafar Ehtesham
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310, India.
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Wadhawan M, Ahmad F, Yadav S, Rathaur S. Proteomic Analysis Reveals Differential Protein Expression Induced by Inhibition of Prolyl Oligopeptidase in Filarial Parasites. Protein J 2022; 41:613-624. [PMID: 36271977 DOI: 10.1007/s10930-022-10080-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 11/24/2022]
Abstract
Prolyl oligopeptidase (POP) plays a crucial role in the processing and degradation of neuropeptides and regulates inositol trisphosphate (IP3) signaling in mammals. We have reported that POP inhibition leads to IP3-mediated calcium efflux leading to mitochondrial-mediated apoptosis in the filarial parasite Setaria cervi. This study further elucidates the effect of altered calcium homeostasis on the proteome of filarial parasites. Adult parasites were treated with POP's specific inhibitor, Z-Pro-prolinal (ZPP), for 7 h. Cytosolic and mitochondrial proteome was analyzed using 2D gel electrophoresis coupled with MALDI-MS/MS. Phosphoproteins were also analyzed in the cytosolic fraction of the parasites. The phosphoprotein analysis revealed 7, and 9 spots in the cytosolic fraction of control and ZPP-treated parasites, respectively. The two identified protein spots in the treated set were found to be involved in G protein signaling. In cytosolic fraction, 109 and 112 protein spots were observed in control and treated parasites, respectively. Of these, 56 upregulated and 32 downregulated protein spots were observed in the treated set. On the other hand, 50 and 47 protein spots were detected in the mitochondrial fraction of control and treated parasites, respectively. Of these spots, 18 upregulated and 12 down-regulated protein spots were found in treated parasites. In silico analysis showed that the identified proteins were involved in energy metabolism, calcium signaling, stress response, and cytoskeleton organization. These findings correlate with our previous results suggesting the important regulatory role of POP in signaling and different metabolic pathways of filarial parasites.
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Affiliation(s)
- Mohit Wadhawan
- Department of Biochemistry, Institute of Science, Banaras Hindu University, 221005, Varanasi, India
| | - Faiyaz Ahmad
- Department of Biochemistry, Institute of Science, Banaras Hindu University, 221005, Varanasi, India
| | - Smita Yadav
- Department of Biochemistry, Institute of Science, Banaras Hindu University, 221005, Varanasi, India
| | - Sushma Rathaur
- Department of Biochemistry, Institute of Science, Banaras Hindu University, 221005, Varanasi, India.
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Basheeruddin M, Khan S, Ahmed N, Jamal S. Effect of pH on Diclofenac–Lysozyme Interaction: Structural and Functional Aspect. Front Mol Biosci 2022; 9:872905. [PMID: 35898307 PMCID: PMC9309515 DOI: 10.3389/fmolb.2022.872905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/03/2022] [Indexed: 11/15/2022] Open
Abstract
As a nonsteroidal antiinflammatory drug, diclofenac (DCF) is used in the treatment of a variety of human ailments. It has already been reported that the use of this class of drugs for a longer duration is associated with numerous side effects such as cardiovascular implications, reno-medullary complications, etc. In the present study, the effect of DCF on the structure, stability, and function of lysozyme was studied. The study was designed to examine the effect of DCF only at various pH values. Heat-induced denaturation of lysozyme was analyzed in the presence and absence of various molar concentrations of DCF at different pH values. The values of thermodynamic parameters, the midpoint of denaturation (Tm), enthalpy change at Tm (ΔHm), constant pressure heat capacity change (ΔCp), and Gibbs energy change at 25°C (ΔGDo), thus obtained under a given set of conditions (pH and molar concentration of DCF), demonstrated the following 1) DCF destabilized lysozyme with respect of Tm and ΔGDo at all the pH values, 2) the magnitude of protein destabilization is lesser at acidic pH than at physiological pH, 3) structural changes in lysozyme are less projecting at pH 2.0 than at pH 7.0, and 4) quenching is observed at both pH values. Furthermore, the process of protein destabilization in the presence of DCF is entropically driven.
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Affiliation(s)
| | | | | | - Shazia Jamal
- *Correspondence: Shazia Jamal, , orcid.org/0000-0003-4555-9513
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Jung KH, Kim YG, Kim CM, Ha HJ, Lee CS, Lee JH, Park HH. Wide-open conformation of UDP-MurNc-tripeptide ligase revealed by the substrate-free structure of MurE from Acinetobacter baumannii. FEBS Lett 2020; 595:275-283. [PMID: 33230844 DOI: 10.1002/1873-3468.14007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/22/2020] [Accepted: 11/20/2020] [Indexed: 12/13/2022]
Abstract
MurE ligase catalyzes the attachment of meso-diaminopimelic acid to the UDP-MurNAc-l -Ala-d -Glu using ATP and producing UDP-MurNAc-l -Ala-d -Glu-meso-A2 pm during bacterial cell wall biosynthesis. Owing to the critical role of this enzyme, MurE is considered an attractive target for antibacterial drugs. Despite extensive studies on MurE ligase, the structural dynamics of its conformational changes are still elusive. In this study, we present the substrate-free structure of MurE from Acinetobacter baumannii, which is an antibiotic-resistant superbacterium that has threatened global public health. The structure revealed that MurE has a wide-open conformation and undergoes wide-open, intermediately closed, and fully closed dynamic conformational transition. Unveiling structural dynamics of MurE will help to understand the working mechanism of this ligase and to design next-generation antibiotics targeting MurE.
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Affiliation(s)
- Kyoung Ho Jung
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Korea.,College of Pharmacy, Chung-Ang University, Seoul, Korea
| | - Yeon-Gil Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Korea
| | - Chang Min Kim
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Korea.,College of Pharmacy, Chung-Ang University, Seoul, Korea
| | - Hyun Ji Ha
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Korea.,College of Pharmacy, Chung-Ang University, Seoul, Korea
| | - Chang Sup Lee
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, Korea
| | - Jun Hyuck Lee
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon, Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, Korea
| | - Hyun Ho Park
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, Korea.,College of Pharmacy, Chung-Ang University, Seoul, Korea
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Structural and conformational behavior of MurE ligase from Salmonella enterica serovar Typhi at different temperature and pH conditions. Int J Biol Macromol 2020; 150:389-399. [DOI: 10.1016/j.ijbiomac.2020.01.306] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 11/20/2022]
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