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Nassiri M, Ghovvati S, Gharouni M, Tahmoorespur M, Bahrami AR, Dehghani H. Engineering Human Pancreatic RNase 1 as an Immunotherapeutic Agent for Cancer Therapy Through Computational and Experimental Studies. Protein J 2024; 43:316-332. [PMID: 38145445 DOI: 10.1007/s10930-023-10171-z] [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] [Accepted: 11/20/2023] [Indexed: 12/26/2023]
Abstract
Most plant and bacterial toxins are highly immunogenic with non-specific toxic effects. Human ribonucleases are thought to provide a promising basis for reducing the toxic agent's immunogenic properties, which are candidates for cancer therapy. In the cell, the ribonuclease inhibitor (RI) protein binds to the ribonuclease enzyme and forms a tight complex. This study aimed to engineer and provide a gene construct encoding an improved version of Human Pancreatic RNase 1 (HP-RNase 1) to reduce connection to RI and modulate the immunogenic effects of immunotoxins. To further characterize the interaction complex of HP-RNase 1 and RI, we established various in silico and in vitro approaches. These methods allowed us to specifically monitor interactions within native and engineered HP-RNase 1/RI complexes. In silico research involved molecular dynamics (MD) simulations of native and mutant HP-RNase 1 in their free form and when bound to RI. For HP-RNase 1 engineering, we designed five mutations (K8A/N72A/N89A/R92D/E112/A) based on literature studies, as this combination proved effective for the intended investigation. Then, the cDNA encoding HP-RNase 1 was generated by RT-PCR from blood and cloned into the pSYN2 expression vector. Consequently, wild-type and the engineered HP-RNase 1 were over-expressed in E. coli TG1 and purified using an IMAC column directed against a poly-his tag. The protein products were detected by SDS-PAGE and Western blot analysis. HP-RNase 1 catalytic activity, in the presence of various concentrations of RI, demonstrated that the mutated version of the protein is able to escape the ribonuclease inhibitor and target the RNA substrate 2.5 folds more than that of the wild type. From these data, we tend to suggest the engineered recombinant HP-RNase 1 potentially as a new immunotherapeutic agent for application in human cancer therapy.
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Affiliation(s)
- Mohammadreza Nassiri
- Department of Animal Science, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Shahrokh Ghovvati
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, 41635-1314, Rasht, Guilan, Iran.
| | - Marzieh Gharouni
- Department of Biochemistry, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Mojtaba Tahmoorespur
- Department of Animal Science, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmad Reza Bahrami
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Molecular Cell Biology, College of Applied Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hesam Dehghani
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Physiology, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
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Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily. Structure 2018; 26:426-436.e3. [PMID: 29478822 DOI: 10.1016/j.str.2018.01.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/06/2017] [Accepted: 01/24/2018] [Indexed: 11/21/2022]
Abstract
Enzyme superfamily members that share common chemical and/or biological functions also share common features. While the role of structure is well characterized, the link between enzyme function and dynamics is not well understood. We present a systematic characterization of intrinsic dynamics of over 20 members of the pancreatic-type RNase superfamily, which share a common structural fold. This study is motivated by the fact that the range of chemical activity as well as molecular motions of RNase homologs spans over 105 folds. Dynamics was characterized using a combination of nuclear magnetic resonance experiments and computer simulations. Phylogenetic clustering led to the grouping of sequences into functionally distinct subfamilies. Detailed characterization of the diverse RNases showed conserved dynamical traits for enzymes within subfamilies. These results suggest that selective pressure for the conservation of dynamical behavior, among other factors, may be linked to the distinct chemical and biological functions in an enzyme superfamily.
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Gagné D, Narayanan C, Bafna K, Charest LA, Agarwal PK, Doucet N. Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:143-149. [PMID: 28271277 PMCID: PMC5589483 DOI: 10.1007/s12104-017-9736-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
Eight active canonical members of the pancreatic-like ribonuclease A (RNase A) superfamily have been identified in human. All structural homologs share similar RNA-degrading functions, while also cumulating other various biological activities in different tissues. The functional homologs eosinophil-derived neurotoxin (EDN, or RNase 2) and eosinophil cationic protein (ECP, or RNase 3) are known to be expressed and secreted by eosinophils in response to infection, and have thus been postulated to play an important role in host defense and inflammatory response. We recently initiated the biophysical and dynamical investigation of several vertebrate RNase homologs and observed that clustering residue dynamics appear to be linked with the phylogeny and biological specificity of several members. Here we report the 1H, 13C and 15N backbone resonance assignments of human EDN (RNase 2) and its molecular dynamics simulation on the microsecond timescale, providing means to pursue this comparative atomic-scale functional and dynamical analysis by NMR and computation over multiple time frames.
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Affiliation(s)
- Donald Gagné
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Khushboo Bafna
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Laurie-Anne Charest
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Pratul K Agarwal
- Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
- PROTEO, The Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, 1045 Avenue de la Médecine, Quebec, QC, G1V 0A6, Canada.
- GRASP, The Groupe de recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada.
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