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Elder JJH, Papadopoulos R, Hayne CK, Stanley RE. The making and breaking of tRNAs by ribonucleases. Trends Genet 2024; 40:511-525. [PMID: 38641471 DOI: 10.1016/j.tig.2024.03.007] [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: 02/08/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Ribonucleases (RNases) play important roles in supporting canonical and non-canonical roles of tRNAs by catalyzing the cleavage of the tRNA phosphodiester backbone. Here, we highlight how recent advances in cryo-electron microscopy (cryo-EM), protein structure prediction, reconstitution experiments, tRNA sequencing, and other studies have revealed new insight into the nucleases that process tRNA. This represents a very diverse group of nucleases that utilize distinct mechanisms to recognize and cleave tRNA during different stages of a tRNA's life cycle including biogenesis, fragmentation, surveillance, and decay. In this review, we provide a synthesis of the structure, mechanism, regulation, and modes of tRNA recognition by tRNA nucleases, along with open questions for future investigation.
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Affiliation(s)
- Jessica J H Elder
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Ry Papadopoulos
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA; Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Cassandra K Hayne
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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2
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Zhou JS, Wen HL, Yu MJ. Mechanism Analysis of Antimicrobial Peptide NoPv1 Related to Potato Late Blight through a Computer-Aided Study. Int J Mol Sci 2024; 25:5312. [PMID: 38791351 PMCID: PMC11121460 DOI: 10.3390/ijms25105312] [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: 04/07/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Phytophthora infestans (Mont.) de Bary, the oomycotic pathogen responsible for potato late blight, is the most devastating disease of potato production. The primary pesticides used to control oomycosis are phenyl amide fungicides, which cause environmental pollution and toxic residues harmful to both human and animal health. To address this, an antimicrobial peptide, NoPv1, has been screened to target Plasmopara viticola cellulose synthase 2 (PvCesA2) to inhibit the growth of Phytophthora infestans (P. infestans). In this study, we employed AlphaFold2 to predict the three-dimensional structure of PvCesA2 along with NoPv peptides. Subsequently, utilizing computational methods, we dissected the interaction mechanism between PvCesA2 and these peptides. Based on this analysis, we performed a saturation mutation of NoPv1 and successfully obtained the double mutants DP1 and DP2 with a higher affinity for PvCesA2. Meanwhile, dynamics simulations revealed that both DP1 and DP2 utilize a mechanism akin to the barrel-stave model for penetrating the cell membrane. Furthermore, the predicted results showed that the antimicrobial activity of DP1 was superior to that of NoPv1 without being toxic to human cells. These findings may offer insights for advancing the development of eco-friendly pesticides targeting various oomycete diseases, including late blight.
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Affiliation(s)
- Jiao-Shuai Zhou
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China;
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Yangtze Delta Region Academy, Beijing Institute of Technology, Jiaxing 314019, China
| | - Hong-Liang Wen
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China;
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Yangtze Delta Region Academy, Beijing Institute of Technology, Jiaxing 314019, China
| | - Ming-Jia Yu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China;
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3
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Liu T, Liu J. Integration analysis of single-cell transcriptome reveals specific monocyte subsets associated with melanoma brain and leptomeningeal metastasis. Skin Res Technol 2024; 30:e13710. [PMID: 38616506 PMCID: PMC11016815 DOI: 10.1111/srt.13710] [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: 03/12/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Melanoma central nervous system (CNS) metastasis remains a leading cause of patient mortality, and the underlying pathological mechanism has not been fully elucidated, leading to a lack of effective therapeutic strategies. MATERIALS AND METHODS In this study, we conducted an integrated analysis of single-cell transcriptomic data related to melanoma brain metastasis (MBM) and leptomeningeal metastasis (LMM). We focused on differences of subset composition and molecular expression of monocytes in blood, primary tumor, brain metastases, and leptomeningeal metastases. RESULTS Significant differences were observed among monocytes in blood, primary tumor, and different CNS metastatic tissues, particularly in terms of subset differentiation and gene expression patterns. Subsequent analysis revealed the upregulation of cell proportions of six monocyte subsets in brain metastasis and leptomeningeal metastasis. Based on differential gene analysis, four of these subsets exhibited increased expression of factors promoting tumor migration and survival, including AREG+ monocytes (AREG, EREG, THBS1), FABP5+ monocytes (SPP1, CCL2, CTSL), and CXCL3+ monocytes (CXCL3, IL8, IL1B). The proportions of TPSB2+ monocytes (IL32, CCL5) were notably elevated in melanoma leptomeningeal metastasis tissues. Pathway analysis indicated the activation of signaling pathways such as NOD-like receptors, NFκB, and Toll-like receptors in these metastasis-related subsets. CONCLUSION Our findings elucidate that AREG+, FABP5+ and CXCL3+ monocytes are associated with brain metastasis and TPSB2+ monocytes are associated with leptomeningeal metastasis in melanoma, which may be contribute to the development of therapeutic strategies focusing on monocytes or cytokines for melanoma CNS metastasis.
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Affiliation(s)
- Tao Liu
- Department of General Surgerythe First People's Hospital of Shuangliu DistrictChengduChina
| | - Jian‐Ping Liu
- Department of General Surgerythe First People's Hospital of Shuangliu DistrictChengduChina
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4
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Di Cera E. A simple method to resolve rate constants when the binding mechanism obeys induced fit or conformational selection. J Biol Chem 2024; 300:107131. [PMID: 38432634 PMCID: PMC10979105 DOI: 10.1016/j.jbc.2024.107131] [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: 01/02/2024] [Revised: 02/10/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024] Open
Abstract
Many interactions involving a ligand and its molecular target are studied by rapid kinetics using a stopped-flow apparatus. Information obtained from these studies is often limited to a single, saturable relaxation that is insufficient to resolve all independent rate constants even for a two-step mechanism of binding obeying induced fit (IF) or conformational selection (CS). We introduce a simple method of general applicability where this limitation is overcome. The method accurately reproduces the rate constants for ligand binding to the serine protease thrombin determined independently from the analysis of multiple relaxations. Application to the inactive zymogen precursor of thrombin, prethrombin-2, resolves all rate constants for a binding mechanism of IF or CS from a single, saturable relaxation. Comparison with thrombin shows that the prethrombin-2 to thrombin conversion enhances ligand binding to the active site not by improving accessibility through the value of kon but by reducing the rate of dissociation koff. The conclusion holds regardless of whether binding is interpreted in terms of IF or CS and has general relevance for the mechanism of zymogen activation of serine proteases. The method also provides a simple test of the validity of IF and CS and indicates when more complex mechanisms of binding should be considered.
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Affiliation(s)
- Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.
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5
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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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6
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Wralstad EC, Raines RT. Sensitive detection of SARS-CoV-2 main protease 3CL pro with an engineered ribonuclease zymogen. Protein Sci 2024; 33:e4916. [PMID: 38501598 PMCID: PMC10949392 DOI: 10.1002/pro.4916] [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: 10/31/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 03/20/2024]
Abstract
Alongside vaccines and antiviral therapeutics, diagnostic tools are a crucial aid in combating the COVID-19 pandemic caused by the etiological agent SARS-CoV-2. All common assays for infection rely on the detection of viral sub-components, including structural proteins of the virion or fragments of the viral genome. Selective pressure imposed by human intervention of COVID-19 can, however, induce viral mutations that decrease the sensitivity of diagnostic assays based on biomolecular structure, leading to an increase in false-negative results. In comparison, mutations are unlikely to alter the function of viral proteins, and viral machinery is under less selective pressure from vaccines and therapeutics. Accordingly, diagnostic assays that rely on biomolecular function can be more robust than ones that rely on biopolymer structure. Toward this end, we used a split intein to create a circular ribonuclease zymogen that is activated by the SARS-CoV-2 main protease, 3CLpro . Zymogen activation by 3CLpro leads to a >300-fold increase in ribonucleolytic activity, which can be detected with a highly sensitive fluorogenic substrate. This coupled assay can detect low nanomolar concentrations of 3CLpro within a timeframe comparable to that of common antigen-detection protocols. More generally, the concept of detecting a protease by activating a ribonuclease could be the basis of diagnostic tools for other indications.
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Affiliation(s)
- Evans C. Wralstad
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Ronald T. Raines
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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Ramzan A, Yousaf MA, Rashid MU, Basheera S, Malkani N. In-silico prediction of TGF-β1 non-synonymous variants and their impact on binding affinity to Fresolimumab. J Biomol Struct Dyn 2023:1-14. [PMID: 37817532 DOI: 10.1080/07391102.2023.2268198] [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: 05/02/2023] [Accepted: 10/03/2023] [Indexed: 10/12/2023]
Abstract
TGF-β1 is a potent immunoregulatory cytokine that plays diverse roles in development, bone healing, fibrosis, and cancer. However, characterizing TGF-β1 gene variants is challenging because the structural and functional consequences of these variants are still undetermined. In this study, we aimed to perform an in-silico analysis of TGF-β1 non-synonymous variants and their pathogenic effects on the TGF-β1 protein. A total of 10,252 TGF-β1 SNPs were collected from the NCBI dbSNP database and in-silico tools (SIFT, PROVEAN, Mutation Taster, ClinVar, PolyPhen-2, CScape, MutPred, and ConSurf) were used. The in-silico predicted potential variants were further investigated for their binding to the TGF-β1 targeting drug "Fresolimumab". Molecular docking was performed using HADDOCK and confirmed by PRODIGY and PDBsum. The in-silico analysis predicted four potential TGF-β1 nsSNPs: E47G in the LAP domain of the propeptide and I22T, L28F, and E35D in the mature TGF-β1 peptide. HADDOCK and molecular dynamics simulations revealed that the I22T and E35D variants have higher binding affinity for Fresolimumab as compared to the wild type and L28F variants. Molecular dynamics simulations (100 ns) and principal component analysis showed that TGF-β1 variants influenced the protein structure and caused variations in the internal dynamics of protein complexes with the antibody. Among them, the E35D variant significantly destabilized the TGF-β1 protein structure, resulting in rearrangement in the binding site and affecting the interactions with the Fresolimumab. This study identified four variants that can affect the TGF-β1 protein structure and result in functional consequences such as impaired response to Fresolimumab.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ammara Ramzan
- Department of Zoology, GC University, Lahore, Pakistan
| | - Muhammad Abrar Yousaf
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Muhammad Usman Rashid
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | - Shefin Basheera
- Department of Biotechnology and Bioinformatics, Thiruvananthapuram, India
| | - Naila Malkani
- Department of Zoology, GC University, Lahore, Pakistan
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Noro I, Bettin I, Fasoli S, Smania M, Lunardi L, Giannini M, Andreoni L, Montioli R, Gotte G. Human RNase 1 can extensively oligomerize through 3D domain swapping thanks to the crucial contribution of its C-terminus. Int J Biol Macromol 2023; 249:126110. [PMID: 37536419 DOI: 10.1016/j.ijbiomac.2023.126110] [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: 04/24/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
Human ribonuclease (RNase) 1 and bovine RNase A are the proto-types of the secretory "pancreatic-type" (pt)-RNase super-family. RNase A can oligomerize through the 3D domain swapping (DS) mechanism upon acetic acid (HAc) lyophilisation, producing enzymatically active oligomeric conformers by swapping both N- and C-termini. Also some RNase 1 mutants were found to self-associate through 3D-DS, however forming only N-swapped dimers. Notably, enzymatically active dimers and larger oligomers of wt-RNase 1 were collected here, in higher amount than RNase A, from HAc lyophilisation. In particular, RNase 1 self-associates through the 3D-DS of its N-terminus and, at a higher extent, of the C-terminus. Since RNase 1 is four-residues longer than RNase A, we further analyzed its oligomerization tendency in a mutant lacking the last four residues. The C-terminus role has been investigated also in amphibian onconase (ONC®), a pt-RNase that can form only a N-swapped dimer, since its C-terminus, that is three-residues longer than RNase A, is locked by a disulfide bond. While ONC mutants designed to unlock or cut this constraint were almost unable to dimerize, the RNase 1 mutant self-associated at a higher extent than the wt, suggesting a specific role of the C-terminus in the oligomerization of different RNases. Overall, RNase 1 reaches here the highest ability, among pt-RNases, to extensively self-associate through 3D-DS, paving the way for new investigations on the structural and biological properties of its oligomers.
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Affiliation(s)
- Irene Noro
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Ilaria Bettin
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Sabrina Fasoli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Marcello Smania
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Luca Lunardi
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Michele Giannini
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Leonardo Andreoni
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Riccardo Montioli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
| | - Giovanni Gotte
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
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Wang Y, Wang T, Chen X, Lu Y. IRES-mediated Pichia pastoris cell-free protein synthesis. BIORESOUR BIOPROCESS 2023; 10:35. [PMID: 38647944 PMCID: PMC10992869 DOI: 10.1186/s40643-023-00653-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/15/2023] [Indexed: 04/25/2024] Open
Abstract
Cell-free protein synthesis (CFPS) system is an ideal platform for fast and convenient protein research and has been used for macromolecular assembly, unnatural amino acid embedding, glycoprotein production, and more. To realize the construction of an efficient eukaryotic CFPS platform with the advantages of low cost and short time, a CFPS system based on the yeast Pichia pastoris was built in this study. The internal ribosomal entry site (IRES) can independently initiate translation and thus promote protein synthesis. The Kozak sequences can facilitate translation initiation. Therefore, the screening of IRES and its combination with Kozak was performed, in which cricket paralysis virus (CRPV) exhibited as the best translation initiation element from 14 different IRESs. Furthermore, the system components and reaction environment were explored. The protein yield was nearly doubled by the addition of RNase inhibitor. The cell extract amount, energy regeneration system (phosphocreatine and phosphocreatine kinase), and metal ions (K+ and Mg2+) were optimized to achieve the best protein synthesis yield. This P. pastoris CFPS system can extend the eukaryotic CFPS platform, providing an enabling technology for fast prototyping design and functional protein synthesis.
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Affiliation(s)
- Yanan Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Ting Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xinjie Chen
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China.
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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Mahmood T, Shahbaz A, Hussain N, Ali R, Bashir H, Rizwan K. Recent advancements in fusion protein technologies in oncotherapy: A review. Int J Biol Macromol 2023; 230:123161. [PMID: 36610574 DOI: 10.1016/j.ijbiomac.2023.123161] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/01/2023] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
Cancer is a complicated, adaptable, and heterogeneous disease caused by a wide variety of genetic changes that might impair ability of cells to function normally. The majority of the tumors can only be shrunk using conventional oncology therapies like chemotherapy, radiation, and surgical resection, and the tumor often recurs. The inability of conventional cancer therapies to completely destroy the Cancer Stem Cells (CSCs) that otherwise lead to therapy resistance is thus addressed by therapeutic approaches that concentrate on targeting CSCs and their micro-environmental niche. In this review, we summarize approaches that are used for the development of fusion proteins and their therapeutic applications for treating cancer. The main purpose of making advancements towards the fusion technology instead of using conventional treatment methods is to achieve a prolonged half-life of the therapeutic drugs. The fusion of drugs to the immune response enhancing cytokines or the fusion of antibody and cytokines not only increases half-life but also increase the stability of the anti-tumor drug. Several molecules including different fragments of antibodies, cytokines, Human Serum Albumin, transferrin, XTEN polymers, Elastin-like polypeptides (ELPs) can be employed as a fusion partner and the resulting fusion proteins are reported to show enhanced anti-tumor response.
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Affiliation(s)
- Tehreem Mahmood
- Department of Biotechnology, Quaid-i-azam University, Islamabad, Pakistan
| | - Areej Shahbaz
- Center for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Nazim Hussain
- Center for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan.
| | - Rahat Ali
- Department of Chemistry, University of Agriculture Faisalabad, Pakistan
| | - Hamid Bashir
- Center for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Komal Rizwan
- Department of Chemistry, University of Sahiwal, Sahiwal 57000, Pakistan.
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11
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Skolnick J, Zhou H. Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein-Protein Interactions. J Phys Chem B 2022; 126:6853-6867. [PMID: 36044742 PMCID: PMC9484464 DOI: 10.1021/acs.jpcb.2c04525] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/18/2022] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions (PPIs) and protein-metabolite interactions play a key role in many biochemical processes, yet they are often viewed as being independent. However, the fact that small molecule drugs have been successful in inhibiting PPIs suggests a deeper relationship between protein pockets that bind small molecules and PPIs. We demonstrate that 2/3 of PPI interfaces, including antibody-epitope interfaces, contain at least one significant small molecule ligand binding pocket. In a representative library of 50 distinct protein-protein interactions involving hundreds of mutations, >75% of hot spot residues overlap with small molecule ligand binding pockets. Hence, ligand binding pockets play an essential role in PPIs. In representative cases, evolutionary unrelated monomers that are involved in different multimeric interactions yet share the same pocket are predicted to bind the same metabolites/drugs; these results are confirmed by examples in the PDB. Thus, the binding of a metabolite can shift the equilibrium between monomers and multimers. This implicit coupling of PPI equilibria, termed "metabolic entanglement", was successfully employed to suggest novel functional relationships among protein multimers that do not directly interact. Thus, the current work provides an approach to unify metabolomics and protein interactomics.
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Affiliation(s)
- Jeffrey Skolnick
- Center for the Study of Systems
Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, NW, Atlanta, Georgia 30332, United States
| | - Hongyi Zhou
- Center for the Study of Systems
Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, NW, Atlanta, Georgia 30332, United States
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Fernández-Millán P, Vázquez-Monteagudo S, Boix E, Prats-Ejarque G. Exploring the RNase A scaffold to combine catalytic and antimicrobial activities. Structural characterization of RNase 3/1 chimeras. Front Mol Biosci 2022; 9:964717. [PMID: 36188223 PMCID: PMC9515509 DOI: 10.3389/fmolb.2022.964717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Design of novel antibiotics to fight antimicrobial resistance is one of the first global health priorities. Novel protein-based strategies come out as alternative therapies. Based on the structure-function knowledge of the RNase A superfamily we have engineered a chimera that combines RNase 1 highest catalytic activity with RNase 3 unique antipathogen properties. A first construct (RNase 3/1-v1) was successfully designed with a catalytic activity 40-fold higher than RNase 3, but alas in detriment of its anti-pathogenic activity. Next, two new versions of the original chimeric protein were created showing improvement in the antimicrobial activity. Both second generation versions (RNases 3/1-v2 and -v3) incorporated a loop characteristic of RNase 3 (L7), associated to antimicrobial activity. Last, removal of an RNase 1 flexible loop (L1) in the third version enhanced its antimicrobial properties and catalytic efficiency. Here we solved the 3D structures of the three chimeras at atomic resolution by X-ray crystallography. Structural analysis outlined the key functional regions. Prediction by molecular docking of the protein chimera in complex with dinucleotides highlighted the contribution of the C-terminal region to shape the substrate binding cavity and determine the base selectivity and catalytic efficiency. Nonetheless, the structures that incorporated the key features related to RNase 3 antimicrobial activity retained the overall RNase 1 active site conformation together with the essential structural elements for binding to the human ribonuclease inhibitor (RNHI), ensuring non-cytotoxicity. Results will guide us in the design of the best RNase pharmacophore for anti-infective therapies.
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Affiliation(s)
| | | | - Ester Boix
- *Correspondence: Ester Boix, ; Guillem Prats-Ejarque,
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13
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Bovine Pancreatic RNase A: An Insight into the Mechanism of Antitumor Activity In Vitro and In Vivo. Pharmaceutics 2022; 14:pharmaceutics14061173. [PMID: 35745743 PMCID: PMC9229056 DOI: 10.3390/pharmaceutics14061173] [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: 05/04/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 12/04/2022] Open
Abstract
In this investigation, we extensively studied the mechanism of antitumor activity of bovine pancreatic RNase A. Using confocal microscopy, we show that after RNase A penetration into HeLa and B16 cells, a part of the enzyme remains unbound with the ribonuclease inhibitor (RI), resulting in the decrease in cytosolic RNAs in both types of cells and rRNAs in the nucleoli of HeLa cells. Molecular docking indicates the ability of RNase A to form a complex with Ku70/Ku80 heterodimer, and microscopy data confirm its localization mostly inside the nucleus, which may underlie the mechanism of RNase A penetration into cells and its intracellular traffic. RNase A reduced migration and invasion of tumor cells in vitro. In vivo, in the metastatic model of melanoma, RNase A suppressed metastases in the lungs and changed the expression of EMT markers in the tissue adjacent to metastatic foci; this increased Cdh1 and decreased Tjp1, Fn and Vim, disrupting the favorable tumor microenvironment. A similar pattern was observed for all genes except for Fn in metastatic foci, indicating a decrease in the invasive potential of tumor cells. Bioinformatic analysis of RNase-A-susceptible miRNAs and their regulatory networks showed that the main processes modulated by RNase A in the tumor microenvironment are the regulation of cell adhesion and junction, cell cycle regulation and pathways associated with EMT and tumor progression.
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14
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In silico mutational analysis of ACE2 to check the susceptibility of lung cancer patients towards COVID-19. Sci Rep 2022; 12:7798. [PMID: 35552474 PMCID: PMC9098448 DOI: 10.1038/s41598-022-11805-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/25/2022] [Indexed: 11/24/2022] Open
Abstract
Being the second major cause of death worldwide, lung cancer poses a significant threat to the health of patients. This worsened during the era of pandemic since lung cancer is found to be more prone to SARS-CoV-2 infection. Many recent studies imply a high frequency of COVID-19 infection associated severe outcome. However, molecular studies are still lacking in this respect. Hence the current study is designed to investigate the binding affinities of ACE2 lung cancer mutants with the viral spike protein to find the susceptibility of respective mutants carrying patients in catching the virus. Quite interestingly, our study found lesser binding affinities of all the selected mutants thus implying that these cancer patients might be less affected by the virus than others. These results are opposed to the recent studies’ propositions and open new avenues for more in-depth studies.
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15
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Nassiri M, Gopalan V, Vakili-Azghandi M. Modifications of Ribonucleases in Order to Enhance Cytotoxicity in Anticancer Therapy. Curr Cancer Drug Targets 2022; 22:373-387. [PMID: 35240973 DOI: 10.2174/1568009622666220303101005] [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] [Received: 08/20/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 11/22/2022]
Abstract
Ribonucleases (RNases) are a superfamily of enzymes that have been extensively studied since the 1960s. For a long time, this group of secretory enzymes was studied as an important model for protein chemistry such as folding, stability and enzymatic catalysis. Since it was discovered that RNases displayed cytotoxic activity against several types of malignant cells, recent investigation has focused mainly on the biological functions and medical applications of engineered RNases. In this review, we describe structures, functions and mechanisms of antitumor activity of RNases. They operate at the crossroads of transcription and translation, preferentially degrading tRNA. As a result, this inhibits protein synthesis, induces apoptosis and causes death of cancer cells. This effect can be enhanced thousands of times when RNases are conjugated with monoclonal antibodies. Such combinations, called immunoRNases, have demonstrated selective antitumor activity against cancer cells both in vitro and in animal models. This review summarizes the current status of engineered RNases and immunoRNases as promising novel therapeutic agents for different types of cancer. Also, we describe our experimental results from published or previously unpublished research and compare with other scientific information.
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Affiliation(s)
- Mohammadreza Nassiri
- Recombinant Proteins Research Group, The Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, NSW, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology, School of Medicine, Griffith University, Gold Coast, Queensland 4222, Australia
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16
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A Comprehensive Computational Analysis for Identification of a Specific Anti-avian Pathogenic Escherichia coli Peptide. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-021-10360-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Garnett ER, Raines RT. Emerging biological functions of ribonuclease 1 and angiogenin. Crit Rev Biochem Mol Biol 2021; 57:244-260. [PMID: 34886717 DOI: 10.1080/10409238.2021.2004577] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pancreatic-type ribonucleases (ptRNases) are a large family of vertebrate-specific secretory endoribonucleases. These enzymes catalyze the degradation of many RNA substrates and thereby mediate a variety of biological functions. Though the homology of ptRNases has informed biochemical characterization and evolutionary analyses, the understanding of their biological roles is incomplete. Here, we review the functions of two ptRNases: RNase 1 and angiogenin. RNase 1, which is an abundant ptRNase with high catalytic activity, has newly discovered roles in inflammation and blood coagulation. Angiogenin, which promotes neovascularization, is now known to play roles in the progression of cancer and amyotrophic lateral sclerosis, as well as in the cellular stress response. Ongoing work is illuminating the biology of these and other ptRNases.
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Affiliation(s)
- Emily R Garnett
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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18
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Xu J, Miao H, Zou L, Tse Sum Bui B, Haupt K, Pan G. Evolution of Molecularly Imprinted Enzyme Inhibitors: From Simple Activity Inhibition to Pathological Cell Regulation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106657] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingjing Xu
- Center for Molecular Recognition and Biosensing School of Life Sciences Shanghai University Shanghai 200444 P. R. China
| | - Haohan Miao
- Institute for Advanced Materials School of Materials Science and Engineering Jiangsu University Zhenjiang Jiangsu 212013 China
| | - Lihua Zou
- Center for Molecular Recognition and Biosensing School of Life Sciences Shanghai University Shanghai 200444 P. R. China
| | - Bernadette Tse Sum Bui
- Université de Technologie de Compiègne CNRS Enzyme and Cell Engineering Laboratory Rue du Docteur Schweitzer 60203 Compiègne Cedex France
| | - Karsten Haupt
- Université de Technologie de Compiègne CNRS Enzyme and Cell Engineering Laboratory Rue du Docteur Schweitzer 60203 Compiègne Cedex France
| | - Guoqing Pan
- Institute for Advanced Materials School of Materials Science and Engineering Jiangsu University Zhenjiang Jiangsu 212013 China
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19
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Xu J, Miao H, Zou L, Tse Sum Bui B, Haupt K, Pan G. Evolution of Molecularly Imprinted Enzyme Inhibitors: From Simple Activity Inhibition to Pathological Cell Regulation. Angew Chem Int Ed Engl 2021; 60:24526-24533. [PMID: 34418248 DOI: 10.1002/anie.202106657] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/11/2021] [Indexed: 02/06/2023]
Abstract
Molecular imprinting represents one of the most promising strategies to design artificial enzyme inhibitors. However, the study of molecularly imprinted enzyme inhibitors (MIEIs) remains at a primary stage. Advanced applications of MIEIs for cell regulation have rarely been explored. Using a solid-phase oriented imprinting strategy so as to leave the active site of the enzymes accessible, we synthesized two MIEIs that exhibit high specificity and potent inhibitory effects (inhibition constant at low nM range) towards trypsin and angiogenin. The trypsin MIEI inhibits trypsin activity, tryptic digestion-induced extracellular matrix lysis and cell membrane destruction, indicating its utility in the treatment of active trypsin-dependent cell injury. The angiogenin MIEI blocks cancer cell proliferation by suppressing the ribonuclease activity of angiogenin and decreasing the angiogenin level inside and outside HeLa cells. Our work demonstrates the versatility of MIEIs for both enzyme inhibition and cell fate manipulation, showing their great potential as therapeutic drugs in biomedicine.
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Affiliation(s)
- Jingjing Xu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Haohan Miao
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Lihua Zou
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Bernadette Tse Sum Bui
- Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue du Docteur Schweitzer, 60203, Compiègne Cedex, France
| | - Karsten Haupt
- Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue du Docteur Schweitzer, 60203, Compiègne Cedex, France
| | - Guoqing Pan
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
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20
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Windsor IW, Dudley DM, O'Connor DH, Raines RT. Ribonuclease zymogen induces cytotoxicity upon HIV-1 infection. AIDS Res Ther 2021; 18:77. [PMID: 34702287 PMCID: PMC8549155 DOI: 10.1186/s12981-021-00399-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 10/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Targeting RNA is a promising yet underdeveloped modality for the selective killing of cells infected with HIV-1. The secretory ribonucleases (RNases) found in vertebrates have cytotoxic ribonucleolytic activity that is kept in check by a cytosolic ribonuclease inhibitor protein, RI. METHODS We engineered amino acid substitutions that enable human RNase 1 to evade RI upon its cyclization into a zymogen that is activated by the HIV-1 protease. In effect, the zymogen has an HIV-1 protease cleavage site between the termini of the wild-type enzyme, thereby positioning a cleavable linker over the active site that blocks access to a substrate. RESULTS The amino acid substitutions in RNase 1 diminish its affinity for RI by 106-fold and confer high toxicity for T-cell leukemia cells. Pretreating these cells with the zymogen leads to a substantial drop in their viability upon HIV-1 infection, indicating specific toxicity toward infected cells. CONCLUSIONS These data demonstrate the utility of ribonuclease zymogens as biologic prodrugs.
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Affiliation(s)
- Ian W Windsor
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Dawn M Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
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21
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Basit A, Karim AM, Asif M, Ali T, Lee JH, Jeon JH, Rehman SU, Lee SH. Designing Short Peptides to Block the Interaction of SARS-CoV-2 and Human ACE2 for COVID-19 Therapeutics. Front Pharmacol 2021; 12:731828. [PMID: 34512357 PMCID: PMC8430035 DOI: 10.3389/fphar.2021.731828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/17/2021] [Indexed: 12/18/2022] Open
Abstract
To date, the current COVID-19 pandemic caused by SARS-CoV-2 has infected 99.2 million while killed 2.2 million people throughout the world and is still spreading widely. The unavailability of potential therapeutics against this virus urges to search and develop new drugs. SARS-CoV-2 enters human cells by interacting with human angiotensin-converting enzyme 2 (ACE2) receptor expressed on human cell surface through utilizing receptor-binding domain (RBD) of its spike glycoprotein. The RBD is highly conserved and is also a potential target for blocking its interaction with human cell surface receptor. We designed short peptides on the basis of our previously reported truncated ACE2 (tACE2) for increasing the binding affinity as well as the binding interaction network with RBD. These peptides can selectively bind to RBD with much higher affinities than the cell surface receptor. Thus, these can block all the binding residues required for binding to cell surface receptor. We used selected amino acid regions (21–40 and 65–75) of ACE2 as scaffold for the de novo peptide design. Our designed peptide Pep1 showed interactions with RBD covering almost all of its binding residues with significantly higher binding affinity (−13.2 kcal mol−1) than the cell surface receptor. The molecular dynamics (MD) simulation results showed that designed peptides form a stabilized complex with RBD. We suggest that blocking the RBD through de novo designed peptides can serve as a potential candidate for COVID-19 treatment after further clinical investigations.
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Affiliation(s)
- Abdul Basit
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Asad Mustafa Karim
- Department of Bioscience and Biotechnology, The University of Suwon, Hwaseong, South Korea
| | - Muhammad Asif
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Tanveer Ali
- Department of Host Defense, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Jung Hun Lee
- National Leading Research Laboratory, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Jeong Ho Jeon
- National Leading Research Laboratory, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Shafiq Ur Rehman
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Sang Hee Lee
- National Leading Research Laboratory, Department of Biological Sciences, Myongji University, Yongin, South Korea
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22
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Basit A, Ali T, Rehman SU. Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent. J Biomol Struct Dyn 2021. [PMID: 32396773 DOI: 10.1080/07391102.07392020.01768150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
The current pandemic of Covid-19 caused by SARS-CoV-2 is continued to spread globally and no potential drug or vaccine against it is available. Spike (S) glycoprotein is the structural protein of SARS-CoV-2 located on the envelope surface, involve in interaction with angiotensin converting enzyme 2 (ACE2), a cell surface receptor, followed by entry into the host cell. Thereby, blocking the S glycoprotein through potential inhibitor may interfere its interaction with ACE2 and impede its entry into the host cell. Here, we present a truncated version of human ACE2 (tACE2), comprising the N terminus region of the intact ACE2 from amino acid position 21-119, involved in binding with receptor binding domain (RBD) of SARS-CoV-2. We analyzed the in-silico potential of tACE2 to compete with intact ACE2 for binding with RBD. The protein-protein docking and molecular dynamic simulation showed that tACE2 has higher binding affinity for RBD and form more stabilized complex with RBD than the intact ACE2. Furthermore, prediction of tACE2 soluble expression in E. coli makes it a suitable candidate to be targeted for Covid-19 therapeutics. This is the first MD simulation based findings to provide a high affinity protein inhibitor for SARS-CoV-2 S glycoprotein, an important target for drug designing against this unprecedented challenge.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdul Basit
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Tanveer Ali
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Shafiq Ur Rehman
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
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23
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Lee J, Lee M, Lee K. Trans-acting regulators of ribonuclease activity. J Microbiol 2021; 59:341-359. [PMID: 33779951 DOI: 10.1007/s12275-021-0650-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 12/16/2022]
Abstract
RNA metabolism needs to be tightly regulated in response to changes in cellular physiology. Ribonucleases (RNases) play an essential role in almost all aspects of RNA metabolism, including processing, degradation, and recycling of RNA molecules. Thus, living systems have evolved to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. In addition, various trans-acting regulators of RNase activity have been discovered in recent years. This review focuses on the physiological roles and underlying mechanisms of trans-acting regulators of RNase activity.
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Affiliation(s)
- Jaejin Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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24
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Batkhishig D, Enkhbayar P, Kretsinger RH, Matsushima N. A crucial residue in the hydrophobic core of the solenoid structure of leucine rich repeats. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140631. [PMID: 33631375 DOI: 10.1016/j.bbapap.2021.140631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023]
Abstract
Leucine rich repeats (LRRs) with 20-30 residues form a super helix arrangement. Individual LRRs are separated into a highly conserved segment with a highly conserved (HCS) and a variable segment (VS). In LRRs short β-strands in HCS stack in parallel, while VS adopts various secondary structures. Among eleven classes recognized, only RI-like, Cysteine-containing (CC), and GALA classes adopt an α-helix. However, the repeat unit lengths are usually different from each other. We performed some analyses based on the atomic coordinates in the known LRR structures. In the VS consensuses of the three classes, position 8 in the VS part is, in common, occupied by conserved aliphatic residue adopting an α-helix. This aliphatic residue is near to the two conserved hydrophobic residues at position 4 (in the center of β-strands) in two adjacent HCS parts. The conserved aliphatic residue plays a crucial role to preserve two parallel β-strands.
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Affiliation(s)
- Dashdavaa Batkhishig
- Department of Physics, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar 210648, Mongolia
| | - Purevjav Enkhbayar
- Laboratory of Bioinformatics and Systems Biology, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 210646, Mongolia.
| | - Robert H Kretsinger
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Norio Matsushima
- Division of Bioinformatics, Institute of Tandem Repeats, Noboribetsu 059-0464, Japan; Center for Medical Education, Sapporo Medical University, Sapporo 060-8556, Japan.
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25
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Lee J, Lee M, Lee K. Trans-acting regulators of ribonuclease activity. J Microbiol 2021:10.1007/s12275-021-0650-3. [PMID: 33565052 DOI: 10.1007/s12275-021-0650-3] [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: 12/11/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022]
Abstract
RNA metabolism needs to be tightly regulated in response to changes in cellular physiology. Ribonucleases (RNases) play an essential role in almost all aspects of RNA metabolism, including processing, degradation, and recycling of RNA molecules. Thus, living systems have evolved to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. In addition, various trans-acting regulators of RNase activity have been discovered in recent years. This review focuses on the physiological roles and underlying mechanisms of trans-acting regulators of RNase activity.
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Affiliation(s)
- Jaejin Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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26
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Sayers J, Wralstad EC, Raines RT. Semisynthesis of Human Ribonuclease-S. Bioconjug Chem 2020; 32:82-87. [PMID: 33296182 DOI: 10.1021/acs.bioconjchem.0c00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since its conception, the ribonuclease S complex (RNase S) has led to historic discoveries in protein chemistry, enzymology, and related fields. Derived by the proteolytic cleavage of a single peptide bond in bovine pancreatic ribonuclease (RNase A), RNase S serves as a convenient and reliable model system for incorporating unlimited functionality into an enzyme. Applications of the RNase S system in biomedicine and biotechnology have, however, been hindered by two shortcomings: (1) the bovine-derived enzyme could elicit an immune response in humans, and (2) the complex is susceptible to dissociation. Here, we have addressed both limitations in the first semisynthesis of an RNase S conjugate derived from human pancreatic ribonuclease and stabilized by a covalent interfragment cross-link. We anticipate that this strategy will enable unprecedented applications of the "RNase-S" system.
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Affiliation(s)
- Jessica Sayers
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Evans C Wralstad
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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27
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Stolwijk JA, Wegener J. Impedance analysis of adherent cells after in situ electroporation-mediated delivery of bioactive proteins, DNA and nanoparticles in µL-volumes. Sci Rep 2020; 10:21331. [PMID: 33288771 PMCID: PMC7721805 DOI: 10.1038/s41598-020-78096-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/18/2020] [Indexed: 01/06/2023] Open
Abstract
Specific intracellular manipulation of animal cells is a persistent goal in experimental cell biology. Such manipulations allow precise and targeted interference with signaling cascades, metabolic pathways, or bi-molecular interactions for subsequent tracking of functional consequences. However, most biomolecules capable of molecular recognition are membrane impermeable. The ability to introduce these molecules into the cytoplasm and then to apply appropriate readouts to monitor the corresponding cell response could prove to be an important research tool. This study describes such an experimental approach combining in situ electroporation (ISE) as a means to efficiently deliver biomolecules to the cytoplasm with an impedance-based, time-resolved analysis of cell status using electric cell-substrate impedance sensing (ECIS). In this approach, gold-film electrodes, deposited on the bottom of regular culture dishes, are used for both electroporation and monitoring. The design of the electrode layout and measurement chamber allows working with sample volumes as small as 10 µL. A miniaturized setup for combined electroporation and impedance sensing (µISE-ECIS) was applied to load different adherent cells with bioactive macromolecules including enzymes, antibodies, nucleic acids and quantum dot nanoparticles. The cell response after loading the cytoplasm with RNase A or cytochrome c (in the presence or absence of caspase inhibitors) was tracked by non-invasive impedance readings in real-time.
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Affiliation(s)
- Judith A Stolwijk
- Institut fuer Analytische Chemie, Chemo- & Biosensorik, Universität Regensburg, Universitaetsstr. 31, 93053, Regensburg, Germany.
| | - Joachim Wegener
- Institut fuer Analytische Chemie, Chemo- & Biosensorik, Universität Regensburg, Universitaetsstr. 31, 93053, Regensburg, Germany.
- Fraunhofer Einrichtung fuer Mikrosysteme und Festkörpertechnologien EMFT, Universitaetsstr. 31, 93053, Regensburg, Germany.
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28
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Di Cera E. Mechanisms of ligand binding. BIOPHYSICS REVIEWS 2020; 1:011303. [PMID: 33313600 PMCID: PMC7714259 DOI: 10.1063/5.0020997] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022]
Abstract
Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.
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Affiliation(s)
- Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
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29
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Bedenbender K, Schmeck BT. Endothelial Ribonuclease 1 in Cardiovascular and Systemic Inflammation. Front Cell Dev Biol 2020; 8:576491. [PMID: 33015070 PMCID: PMC7500176 DOI: 10.3389/fcell.2020.576491] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022] Open
Abstract
The vascular endothelial cell layer forms the inner lining of all blood vessels to maintain proper functioning of the vascular system. However, dysfunction of the endothelium depicts a major issue in context of vascular pathologies, such as atherosclerosis or thrombosis that cause several million deaths per year worldwide. In recent years, the endothelial extracellular endonuclease Ribonuclease 1 (RNase1) was described as a key player in regulation of vascular homeostasis by protecting endothelial cells from detrimental effects of the damage-associated molecular pattern extracellular RNA upon acute inflammation. Despite this protective function, massive dysregulation of RNase1 was observed during prolonged endothelial cell inflammation resulting in progression of several vascular diseases. For the first time, this review article outlines the current knowledge on endothelial RNase1 and its role in function and dysfunction of the endothelium, thereby focusing on the intensive research from recent years: Uncovering the underlying mechanisms of RNase1 function and regulation in response to acute as well as long-term inflammation, the role of RNase1 in context of vascular, inflammatory and infectious diseases and the potential to develop novel therapeutic options to treat these pathologies against the background of RNase1 function in endothelial cells.
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Affiliation(s)
- Katrin Bedenbender
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center, Marburg, Germany
| | - Bernd T. Schmeck
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center, Marburg, Germany
- Department of Pulmonary and Critical Care Medicine, Department of Medicine, University Medical Center Giessen and Marburg, Philipps-University Marburg, Marburg, Germany
- Member of the German Center for Lung Research, Member of the German Center for Infectious Disease Research, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
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30
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Kilgore HR, Latham AP, Ressler VT, Zhang B, Raines RT. Structure and Dynamics of N-Glycosylated Human Ribonuclease 1. Biochemistry 2020; 59:3148-3156. [PMID: 32544330 DOI: 10.1021/acs.biochem.0c00191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Glycosylation is a common modification that can endow proteins with altered physical and biological properties. Ribonuclease 1 (RNase 1), which is the human homologue of the archetypal enzyme RNase A, undergoes N-linked glycosylation at asparagine residues 34, 76, and 88. We have produced the three individual glycoforms that display the core heptasaccharide, Man5GlcNAc2, and analyzed the structure of each glycoform by using small-angle X-ray scattering along with molecular dynamics simulations. The glycan on Asn34 is relatively compact and rigid, donates hydrogen bonds that "cap" the carbonyl groups at the C-terminus of an α-helix, and enhances protein thermostability. In contrast, the glycan on Asn88 is flexible and can even enter the enzymic active site, hindering catalysis. The N-glycosylation of Asn76 has less pronounced consequences. These data highlight the diverse behaviors of Man5GlcNAc2 pendants and provide a structural underpinning to the functional consequences of protein glycosylation.
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Affiliation(s)
- Henry R Kilgore
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Valerie T Ressler
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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31
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Basit A, Ali T, Rehman SU. Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent. J Biomol Struct Dyn 2020; 39:3605-3614. [PMID: 32396773 PMCID: PMC7256354 DOI: 10.1080/07391102.2020.1768150] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The current pandemic of Covid-19 caused by SARS-CoV-2 is continued to spread globally and no potential drug or vaccine against it is available. Spike (S) glycoprotein is the structural protein of SARS-CoV-2 located on the envelope surface, involve in interaction with angiotensin converting enzyme 2 (ACE2), a cell surface receptor, followed by entry into the host cell. Thereby, blocking the S glycoprotein through potential inhibitor may interfere its interaction with ACE2 and impede its entry into the host cell. Here, we present a truncated version of human ACE2 (tACE2), comprising the N terminus region of the intact ACE2 from amino acid position 21-119, involved in binding with receptor binding domain (RBD) of SARS-CoV-2. We analyzed the in-silico potential of tACE2 to compete with intact ACE2 for binding with RBD. The protein-protein docking and molecular dynamic simulation showed that tACE2 has higher binding affinity for RBD and form more stabilized complex with RBD than the intact ACE2. Furthermore, prediction of tACE2 soluble expression in E. coli makes it a suitable candidate to be targeted for Covid-19 therapeutics. This is the first MD simulation based findings to provide a high affinity protein inhibitor for SARS-CoV-2 S glycoprotein, an important target for drug designing against this unprecedented challenge.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdul Basit
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Tanveer Ali
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Shafiq Ur Rehman
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
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32
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Yazhini A, Srinivasan N. How good are comparative models in the understanding of protein dynamics? Proteins 2020; 88:874-888. [PMID: 31999374 DOI: 10.1002/prot.25879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/04/2020] [Accepted: 01/25/2020] [Indexed: 12/27/2022]
Abstract
The 3D structure of a protein is essential to understand protein dynamics. If experimentally determined structure is unavailable, comparative models could be used to infer dynamics. However, the effectiveness of comparative models, compared to experimental structures, in inferring dynamics is not clear. To address this, we compared dynamics features of ~800 comparative models with their crystal structures using normal mode analysis. Average similarity in magnitude, direction, and correlation of residue motions is >0.8 (where value 1 is identical) indicating that the dynamics of models and crystal structures are highly similar. Accuracy of 3D structure and dynamics is significantly higher for models built on multiple and/or high sequence identity templates (>40%). Three-dimensional (3D) structure and residue fluctuations of models are closer to that of crystal structures than to templates (TM score 0.9 vs 0.7 and square inner product 0.92 vs 0.88). Furthermore, long-range molecular dynamics simulations on comparative models of RNase 1 and Angiogenin showed significant differences in the conformational sampling of conserved active-site residues that characterize differences in their activity levels. Similar analyses on two EGFR kinase variant models highlight the effect of mutations on the functional state-specific αC helix motions and these results corroborate with the previous experimental observations. Thus, our study adds confidence to the use of comparative models in understanding protein dynamics.
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Affiliation(s)
- Arangasamy Yazhini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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Gotte G, Menegazzi M. Biological Activities of Secretory RNases: Focus on Their Oligomerization to Design Antitumor Drugs. Front Immunol 2019; 10:2626. [PMID: 31849926 PMCID: PMC6901985 DOI: 10.3389/fimmu.2019.02626] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022] Open
Abstract
Ribonucleases (RNases) are a large number of enzymes gathered into different bacterial or eukaryotic superfamilies. Bovine pancreatic RNase A, bovine seminal BS-RNase, human pancreatic RNase 1, angiogenin (RNase 5), and amphibian onconase belong to the pancreatic type superfamily, while binase and barnase are in the bacterial RNase N1/T1 family. In physiological conditions, most RNases secreted in the extracellular space counteract the undesired effects of extracellular RNAs and become protective against infections. Instead, if they enter the cell, RNases can digest intracellular RNAs, becoming cytotoxic and having advantageous effects against malignant cells. Their biological activities have been investigated either in vitro, toward a number of different cancer cell lines, or in some cases in vivo to test their potential therapeutic use. However, immunogenicity or other undesired effects have sometimes been associated with their action. Nevertheless, the use of RNases in therapy remains an appealing strategy against some still incurable tumors, such as mesothelioma, melanoma, or pancreatic cancer. The RNase inhibitor (RI) present inside almost all cells is the most efficacious sentry to counteract the ribonucleolytic action against intracellular RNAs because it forms a tight, irreversible and enzymatically inactive complex with many monomeric RNases. Therefore, dimerization or multimerization could represent a useful strategy for RNases to exert a remarkable cytotoxic activity by evading the interaction with RI by steric hindrance. Indeed, the majority of the mentioned RNases can hetero-dimerize with antibody derivatives, or even homo-dimerize or multimerize, spontaneously or artificially. This can occur through weak interactions or upon introducing covalent bonds. Immuno-RNases, in particular, are fusion proteins representing promising drugs by combining high target specificity with easy delivery in tumors. The results concerning the biological features of many RNases reported in the literature are described and discussed in this review. Furthermore, the activities displayed by some RNases forming oligomeric complexes, the mechanisms driving toward these supramolecular structures, and the biological rebounds connected are analyzed. These aspects are offered with the perspective to suggest possible efficacious therapeutic applications for RNases oligomeric derivatives that could contemporarily lack, or strongly reduce, immunogenicity and other undesired side-effects.
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Affiliation(s)
- Giovanni Gotte
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Marta Menegazzi
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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Forouharmehr A, Nassiri M, Ghovvati Roudsari S, Javadmanesh A. Production and introduction of a novel immunotoxin based on engineered RNase A for inducing death to Her1-positive cell lines. J Cell Physiol 2019; 235:4679-4687. [PMID: 31663127 DOI: 10.1002/jcp.29346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022]
Abstract
The present study was performed to design an immunotoxin consisting of engineered RNase A and scFv of Cetuximab. To accomplish this study goal, at first to evade RNase A from its inhibitors in the cytoplasm, six amino acids of RNase A were substituted, then the physicochemical features of engineered RNase A were assessed. To investigate the interaction between the engineered RNase A and the ribonuclease inhibitor, protein-protein docking was performed. After engineering the RNase A, it was theoretically conjugated with scFv of Cetuximab using a cleavable linker to produce scFv-engineered RNase A. Then, wild-RNase A (14 kD), engineered RNase A (14 kD) and scFv-engineered RNase A (42 kDa) were expressed in the BL21 (DE3) strain of Escherichia coli and purified by Ni-NTA columns. To confirm the expressed proteins, western blot analysis was performed. The functioning of wild-RNase A and engineered RNase A were investigated by RNA fragmentation assay. Finally, to evaluate the cytotoxicity of scFv-engineered RNase A, a dose-response cytotoxicity assay was performed on Her1-positive and Her1-negative cell lines. The results showed that engineered RNase A could maintain its structure and disulfide bonds and evade its inhibitor. Expression and purification were successfully conducted and both enzymes could degrade yeast RNA. The result of cytotoxicity showed that the engineered immunotoxin could induce cell death to Her1-positive cell lines with an IC50 of 50 nM. It appears that scFv-engineered RNase A can be a promising molecule for use.
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Affiliation(s)
- Ali Forouharmehr
- Department of Animal Science, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.,Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammadreza Nassiri
- Recombinant Proteins Research Group, The Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Ali Javadmanesh
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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35
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Mironova N, Vlassov V. Surveillance of Tumour Development: The Relationship Between Tumour-Associated RNAs and Ribonucleases. Front Pharmacol 2019; 10:1019. [PMID: 31572192 PMCID: PMC6753386 DOI: 10.3389/fphar.2019.01019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/09/2019] [Indexed: 12/14/2022] Open
Abstract
Tumour progression is accompanied by rapid cell proliferation, loss of differentiation, the reprogramming of energy metabolism, loss of adhesion, escape of immune surveillance, induction of angiogenesis, and metastasis. Both coding and regulatory RNAs expressed by tumour cells and circulating in the blood are involved in all stages of tumour progression. Among the important tumour-associated RNAs are intracellular coding RNAs that determine the routes of metabolic pathways, cell cycle control, angiogenesis, adhesion, apoptosis and pathways responsible for transformation, and intracellular and extracellular non-coding RNAs involved in regulation of the expression of their proto-oncogenic and oncosuppressing mRNAs. Considering the diversity/variability of biological functions of RNAs, it becomes evident that extracellular RNAs represent important regulators of cell-to-cell communication and intracellular cascades that maintain cell proliferation and differentiation. In connection with the elucidation of such an important role for RNA, a surge in interest in RNA-degrading enzymes has increased. Natural ribonucleases (RNases) participate in various cellular processes including miRNA biogenesis, RNA decay and degradation that has determined their principal role in the sustention of RNA homeostasis in cells. Findings were obtained on the contribution of some endogenous ribonucleases in the maintenance of normal cell RNA homeostasis, which thus prevents cell transformation. These findings directed attention to exogenous ribonucleases as tools to compensate for the malfunction of endogenous ones. Recently a number of proteins with ribonuclease activity were discovered whose intracellular function remains unknown. Thus, the comprehensive investigation of physiological roles of RNases is still required. In this review we focused on the control mechanisms of cell transformation by endogenous ribonucleases, and the possibility of replacing malfunctioning enzymes with exogenous ones.
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Affiliation(s)
- Nadezhda Mironova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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36
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Windsor IW, Graff CJ, Raines RT. Circular zymogens of human ribonuclease 1. Protein Sci 2019; 28:1713-1719. [PMID: 31306518 PMCID: PMC6699097 DOI: 10.1002/pro.3686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/11/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022]
Abstract
The endogenous production of enzymes as zymogens provides a means to control catalytic activities. Here, we describe the heterologous production of ribonuclease 1 (RNase 1), which is the most prevalent secretory ribonuclease in humans, as a zymogen. In folded RNase 1, the N and C termini flank the enzymic active site. By using intein-mediated cis-splicing, we created circular proteins in which access to the active site of RNase 1 is obstructed by an amino-acid sequence that is recognized by the HIV-1 protease. Installing a sequence that does not perturb the RNase 1 fold led to only modest inactivation. In contrast, the ancillary truncation of residues from each terminus led to a substantial decrease in the catalytic activity of the zymogen with the maintenance of thermostability. For optimized zymogens, activation by HIV-1 protease led to a > 104 -fold increase in ribonucleolytic activity at a rate comparable to that for the cleavage of endogenous viral substrates. Molecular modeling indicated that these zymogens are inactivated by conformational distortion in addition to substrate occlusion. Because protease levels are elevated in many disease states and ribonucleolytic activity can be cytotoxic, RNase 1 zymogens have potential as generalizable prodrugs.
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Affiliation(s)
- Ian W. Windsor
- Department of BiochemistryUniversity of Wisconsin−MadisonMadisonWisconsin
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Crystal J. Graff
- Department of BiochemistryUniversity of Wisconsin−MadisonMadisonWisconsin
| | - Ronald T. Raines
- Department of BiochemistryUniversity of Wisconsin−MadisonMadisonWisconsin
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusetts
- Department of ChemistryUniversity of Wisconsin−MadisonMadisonWisconsin
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37
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Huysmans H, De Temmerman J, Zhong Z, Mc Cafferty S, Combes F, Haesebrouck F, Sanders NN. Improving the Repeatability and Efficacy of Intradermal Electroporated Self-Replicating mRNA. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:388-395. [PMID: 31307005 PMCID: PMC6626868 DOI: 10.1016/j.omtn.2019.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 11/30/2022]
Abstract
Local administration of naked self-replicating mRNA (sr-mRNA) in the skin or muscle using electroporation is effective but hampered by low repeatability. In this manuscript, we demonstrated that intradermal electroporation of sr-mRNA in combination with a protein-based RNase inhibitor increased the expression efficiency, success rate, and repeatability of the data. The RNase inhibitor should be added just before administration because storage of the inhibitor together with the sr-mRNA at −80°C resulted in a partial loss of the beneficial effect. Furthermore, the location of intradermal electroporation also had a major effect on the expression of the sr-mRNA, with the highest and longest expression observed at the tail base of the mice. In contrast with previous work, we did not observe a beneficial effect of calcium ions on the efficacy of naked sr-mRNA after intradermal injection. Finally, another important finding was that the traditional representation of in vivo bioluminescence data as means in logarithmic graphs can mask highly variable data. A more truthful representation can be obtained by showing the individual data points or by displaying median values in combination with interquartile ranges. In conclusion, intradermal sr-mRNA electroporation can be improved by adding an RNase inhibitor and injecting at the tail base.
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Affiliation(s)
- Hanne Huysmans
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Joyca De Temmerman
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Zifu Zhong
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Séan Mc Cafferty
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute (CRIG), Ghent University, Merelbeke, Belgium
| | - Francis Combes
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute (CRIG), Ghent University, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Niek N Sanders
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute (CRIG), Ghent University, Merelbeke, Belgium.
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Ressler VT, Mix KA, Raines RT. Esterification Delivers a Functional Enzyme into a Human Cell. ACS Chem Biol 2019; 14:599-602. [PMID: 30830748 DOI: 10.1021/acschembio.9b00033] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A major hurdle in chemical biology is the delivery of native proteins into the cytosol of mammalian cells. Herein, we report that esterification of the carboxyl groups of an enzyme with a diazo compound enables not only its passage into the cytosol but also the retention of its catalytic activity there. This scenario is demonstrated with human ribonuclease 1, which manifests ribonucleolytic activity that can be cytotoxic. After internalization, the nascent esters are hydrolyzed in situ by endogenous esterases, making the process traceless. This strategy provides unprecedented opportunities for the delivery of functional enzymes into human cells.
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Affiliation(s)
- Valerie T. Ressler
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kalie A. Mix
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Ressler VT, Raines RT. Consequences of the Endogenous N-Glycosylation of Human Ribonuclease 1. Biochemistry 2019; 58:987-996. [PMID: 30633504 DOI: 10.1021/acs.biochem.8b01246] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonuclease 1 (RNase 1) is the most prevalent human homologue of the archetypal enzyme RNase A. RNase 1 contains sequons for N-linked glycosylation at Asn34, Asn76, and Asn88 and is N-glycosylated at all three sites in vivo. The effect of N-glycosylation on the structure and function of RNase 1 is unknown. By using an engineered strain of the yeast Pichia pastoris, we installed a heptasaccharide (Man5GlcNAc2) on the side chain of Asn34, Asn76, and Asn88 to produce the authentic triglycosylated form of human RNase 1. As a glutamine residue is not a substrate for cellular oligosaccharyltransferase, we used strategic asparagine-to-glutamine substitutions to produce the three diglycosylated and three monoglycosylated forms of RNase 1. We found that the N-glycosylation of RNase 1 at any position attenuates its catalytic activity but enhances both its thermostability and its resistance to proteolysis. N-Glycosylation at Asn34 generates the most active and stable glycoforms, in accord with its sequon being highly conserved among vertebrate species. These data provide new insight on the biological role of the N-glycosylation of a human secretory enzyme.
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Affiliation(s)
- Valerie T Ressler
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Ronald T Raines
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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40
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Hoang TT, Tanrikulu IC, Vatland QA, Hoang TM, Raines RT. A Human Ribonuclease Variant and ERK-Pathway Inhibitors Exhibit Highly Synergistic Toxicity for Cancer Cells. Mol Cancer Ther 2018; 17:2622-2632. [PMID: 30282811 DOI: 10.1158/1535-7163.mct-18-0724] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/15/2018] [Accepted: 09/27/2018] [Indexed: 12/20/2022]
Abstract
Pancreatic-type ribonucleases (ptRNases) are prevalent secretory enzymes that catalyze the cleavage of RNA. Ribonuclease inhibitor (RI) is a cytosolic protein that has femtomolar affinity for ptRNases, affording protection from the toxic catalytic activity of ptRNases, which can invade human cells. A human ptRNase variant that is resistant to inhibition by RI is a cytotoxin that is undergoing a clinical trial as a cancer chemotherapeutic agent. We find that the ptRNase and protein kinases in the ERK pathway exhibit strongly synergistic toxicity toward lung cancer cells (including a KRASG12C variant) and melanoma cells (including BRAFV600E variants). The synergism arises from inhibiting the phosphorylation of RI and thereby diminishing its affinity for the ptRNase. These findings link seemingly unrelated cellular processes, and suggest that the use of a kinase inhibitor to unleash a cytotoxic enzyme could lead to beneficial manifestations in the clinic.
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Affiliation(s)
- Trish T Hoang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - I Caglar Tanrikulu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Quinn A Vatland
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Trieu M Hoang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ronald T Raines
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin. .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
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41
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Tavernier Q, Bennana E, Poindessous V, Schaeffer C, Rampoldi L, Pietrancosta N, Pallet N. Regulation of IRE1 RNase activity by the Ribonuclease inhibitor 1 (RNH1). Cell Cycle 2018; 17:1901-1916. [PMID: 30109813 DOI: 10.1080/15384101.2018.1506655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Adaptation to endoplasmic reticulum (ER) stress depends on the activation of the sensor inositol-requiring enzyme 1α (IRE1), an endoribonuclease that splices the mRNA of the transcription factor XBP1 (X-box-binding protein 1). To better understand the protein network that regulates the activity of the IRE1 pathway, we systematically screened the proteins that interact with IRE1 and identified a ribonuclease inhibitor called ribonuclease/angiogenin inhibitor 1 (RNH1). RNH1 is a leucine-rich repeat domains-containing protein that binds to and inhibits ribonucleases. Immunoprecipitation experiments confirmed this interaction. Docking experiments indicated that RNH1 physically interacts with IRE1 through its cytosolic RNase domain. Upon ER stress, the interaction of RNH1 with IRE1 in the ER increased at the expense of the nuclear pool of RNH1. Inhibition of RNH1 expression using siRNA mediated RNA interference upon ER stress led to an increased splicing activity of XBP1. Modulation of IRE1 RNase activity by RNH1 was recapitulated in a cell-free system, suggesting direct regulation of IRE1 by RNH. We conclude that RNH1 attenuates the activity of IRE1 by interacting with its ribonuclease domain. These findings have implications for understanding the molecular mechanism by which IRE1 signaling is attenuated upon ER stress.
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Affiliation(s)
- Quentin Tavernier
- a Institut National de la Santé et de la Recherche Médicale (INSERM) U1147 , Paris , France.,b Paris Descartes University , Paris , France
| | - Evangeline Bennana
- b Paris Descartes University , Paris , France.,c 3P5 Proteomic facility, COMUE Sorbonne Paris Cité , Université Paris Descartes , Paris , France
| | - Virginie Poindessous
- a Institut National de la Santé et de la Recherche Médicale (INSERM) U1147 , Paris , France.,b Paris Descartes University , Paris , France
| | - Celine Schaeffer
- d Molecular Genetics of Renal Disorders Unit, Division of Genetics and Cell Biology , IRCCS San Raffaele Scientific Institute , Milan , Italy
| | - Luca Rampoldi
- d Molecular Genetics of Renal Disorders Unit, Division of Genetics and Cell Biology , IRCCS San Raffaele Scientific Institute , Milan , Italy
| | - Nicolas Pietrancosta
- b Paris Descartes University , Paris , France.,e Centre National pour la Recherche Scientifique (CNRS) U8601 , Paris , France.,f Team Chemistry and Biology, Modeling & Immunology for Therapy , CBMIT, 2MI Platform , Paris , France
| | - Nicolas Pallet
- a Institut National de la Santé et de la Recherche Médicale (INSERM) U1147 , Paris , France.,b Paris Descartes University , Paris , France.,g Clinical Chemistry Department , Hôpital Européen Gorges Pompidou, APHP , Paris , France.,h Plate-forme Proteomique 3P5 , Universite Paris Descartes, Sorbonne Paris Cite , Paris , France
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42
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Trepte P, Kruse S, Kostova S, Hoffmann S, Buntru A, Tempelmeier A, Secker C, Diez L, Schulz A, Klockmeier K, Zenkner M, Golusik S, Rau K, Schnoegl S, Garner CC, Wanker EE. LuTHy: a double-readout bioluminescence-based two-hybrid technology for quantitative mapping of protein-protein interactions in mammalian cells. Mol Syst Biol 2018; 14:e8071. [PMID: 29997244 PMCID: PMC6039870 DOI: 10.15252/msb.20178071] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 06/08/2018] [Accepted: 06/15/2018] [Indexed: 12/12/2022] Open
Abstract
Information on protein-protein interactions (PPIs) is of critical importance for studying complex biological systems and developing therapeutic strategies. Here, we present a double-readout bioluminescence-based two-hybrid technology, termed LuTHy, which provides two quantitative scores in one experimental procedure when testing binary interactions. PPIs are first monitored in cells by quantification of bioluminescence resonance energy transfer (BRET) and, following cell lysis, are again quantitatively assessed by luminescence-based co-precipitation (LuC). The double-readout procedure detects interactions with higher sensitivity than traditional single-readout methods and is broadly applicable, for example, for detecting the effects of small molecules or disease-causing mutations on PPIs. Applying LuTHy in a focused screen, we identified 42 interactions for the presynaptic chaperone CSPα, causative to adult-onset neuronal ceroid lipofuscinosis (ANCL), a progressive neurodegenerative disease. Nearly 50% of PPIs were found to be affected when studying the effect of the disease-causing missense mutations L115R and ∆L116 in CSPα with LuTHy. Our study presents a robust, sensitive research tool with high utility for investigating the molecular mechanisms by which disease-associated mutations impair protein activity in biological systems.
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Affiliation(s)
- Philipp Trepte
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sabrina Kruse
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Simona Kostova
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sheila Hoffmann
- Synaptopathy, German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Alexander Buntru
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Anne Tempelmeier
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Christopher Secker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
- Department of Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Lisa Diez
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Aline Schulz
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Konrad Klockmeier
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Martina Zenkner
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sabrina Golusik
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Kirstin Rau
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Sigrid Schnoegl
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Craig C Garner
- Synaptopathy, German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
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43
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Simões ICM, Coimbra JTS, Neves RPP, Costa IPD, Ramos MJ, Fernandes PA. Properties that rank protein:protein docking poses with high accuracy. Phys Chem Chem Phys 2018; 20:20927-20942. [DOI: 10.1039/c8cp03888k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The development of docking algorithms to predict near-native structures of protein:protein complexes from the structure of the isolated monomers is of paramount importance for molecular biology and drug discovery.
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Affiliation(s)
- Inês C. M. Simões
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - João T. S. Coimbra
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Rui P. P. Neves
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Inês P. D. Costa
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Maria J. Ramos
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Pedro A. Fernandes
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
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44
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Earl CC, Smith MT, Lease RA, Bundy BC. Polyvinylsulfonic acid: A Low-cost RNase inhibitor for enhanced RNA preservation and cell-free protein translation. Bioengineered 2017; 9:90-97. [PMID: 28662363 PMCID: PMC5972934 DOI: 10.1080/21655979.2017.1313648] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The effectiveness and economics of polyvinyl sulfonic acid (PVSA) as a ribonuclease inhibitor for in vitro systems is reported. PVSA was shown to inhibit RNA cleavage in the presence of RNase A as well as in the presence of Escherichia coli lysate, suggesting that PVSA can act as a broader ribonuclease inhibitor. In addition, PVSA was shown to improve the integrity of mRNA transcripts by up to 5-fold in vitro as measured by their translational viability. Improved preservation of mRNA transcripts in the presence of PVSA under common RNA storage conditions is also reported. A cost comparison with commercially available RNAse inhibitors indicates the economic practicality of PVSA which is approximately 1,700 times less expensive than commonly used ribonuclease inhibitors. PVSA can also be separated from RNA by alcohol precipitation for applications that may be sensitive to the presence of PVSA.
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Affiliation(s)
- Conner C Earl
- a Department of Chemical Engineering , Brigham Young University , Provo , UT , USA
| | - Mark T Smith
- a Department of Chemical Engineering , Brigham Young University , Provo , UT , USA
| | - Richard A Lease
- b Department of Chemical and Biomolecular Engineering , The Ohio State University , Columbus OH USA
| | - Bradley C Bundy
- a Department of Chemical Engineering , Brigham Young University , Provo , UT , USA
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45
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Comparative functional analysis of ribonuclease 1 homologs: molecular insights into evolving vertebrate physiology. Biochem J 2017; 474:2219-2233. [PMID: 28495858 DOI: 10.1042/bcj20170173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/30/2017] [Accepted: 05/10/2017] [Indexed: 12/13/2022]
Abstract
Pancreatic-type ribonucleases (ptRNases) comprise a class of highly conserved secretory endoribonucleases in vertebrates. The prototype of this enzyme family is ribonuclease 1 (RNase 1). Understanding the physiological roles of RNase 1 is becoming increasingly important, as engineered forms of the enzyme progress through clinical trials as chemotherapeutic agents for cancer. Here, we present an in-depth biochemical characterization of RNase 1 homologs from a broad range of mammals (human, bat, squirrel, horse, cat, mouse, and cow) and nonmammalian species (chicken, lizard, and frog). We discover that the human homolog of RNase 1 has a pH optimum for catalysis, ability to degrade double-stranded RNA, and affinity for cell-surface glycans that are distinctly higher than those of its homologs. These attributes have relevance for human health. Moreover, the functional diversification of the 10 RNase 1 homologs illuminates the regulation of extracellular RNA and other aspects of vertebrate evolution.
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46
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Yan Y, Yang M, Ji CG, Zhang JZ. Interaction Entropy for Computational Alanine Scanning. J Chem Inf Model 2017; 57:1112-1122. [DOI: 10.1021/acs.jcim.6b00734] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yuna Yan
- State
Key Laboratory for Precision Spectroscopy, School of Chemistry and
Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Maoyou Yang
- College of Mathematics & Physics, Shandong Institute of Light Industry, Jinan, Shandong 250353, China
| | - Chang G. Ji
- State
Key Laboratory for Precision Spectroscopy, School of Chemistry and
Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - John Z.H. Zhang
- State
Key Laboratory for Precision Spectroscopy, School of Chemistry and
Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department
of Chemistry, New York University, New York, New York 10003, United States
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47
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Ohashi A, Murata A, Cho Y, Ichinose S, Sakamaki Y, Nishio M, Hoshi O, Fischer S, Preissner KT, Koyama T. The expression and localization of RNase and RNase inhibitor in blood cells and vascular endothelial cells in homeostasis of the vascular system. PLoS One 2017; 12:e0174237. [PMID: 28329009 PMCID: PMC5362223 DOI: 10.1371/journal.pone.0174237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/06/2017] [Indexed: 02/02/2023] Open
Abstract
RNA may be released from vascular cells including endothelial cells in the event of injury and in vascular disease. Extracellular RNAs have been recognized as novel procoagulant and permeability-increasing factors. Extracellular RNA may function as inflammatory host alarm signals that serve to amplify the defense mechanism, but it may provide important links to thrombus formation. Extracellular RNA is degraded by RNase. We propose that RNase and its inhibitor RNase inhibitor (RI) act as modulators of homeostasis in the vasculature to control the functions of extracellular RNA. We aimed to investigate the expression and localization of RNase 1 and RI in cells that contact blood, such as platelets, mononuclear cells, polymorphonuclear cells, and red blood cells. RNase 1 and RI expression and localization in blood cells were compared with those in the human umbilical vein endothelial cell line, EAhy926. Additionally, we further investigated the effect of thrombin on the expression of RNase 1 and RI in platelets. We used an RNase activity assay, reverse transcription-polymerase chain reaction, western blot, immunocytochemistry, transmission electron microscopy, and immunoelectron microscopy (pre- and post-embedding methods). RNase activity in the supernatant from EAhy926 cells was 50 times than in blood cells (after 60 min). RNase 1 mRNA and protein expression in EAhy926 cells was highest among the cells examined. However, RI mRNA and protein expression was similar in most cell types examined. Furthermore, we observed that RNase 1 and von Willebrand factor were partially colocalized in EAhy926 cells and platelets. In conclusion, we propose that high RNase activity is ordinarily released from endothelial cells to support anticoagulation in the vasculature. On the other hand, platelets and leukocytes within thrombi at sites of vascular injury show very low RNase activity, which may support hemostatic thrombus formation. However, activated platelets and leukocytes may accelerate pathologic thrombus formation.
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Affiliation(s)
- Ayaka Ohashi
- Laboratory Molecular Genetics of Hematology, Field of Applied Laboratory Science, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Aya Murata
- Laboratory Molecular Genetics of Hematology, Field of Applied Laboratory Science, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuichiro Cho
- Anatomy and Physiological Science, Field of Applied Laboratory Science, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shizuko Ichinose
- Instrumental Analysis Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuriko Sakamaki
- Instrumental Analysis Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Miwako Nishio
- Laboratory Molecular Genetics of Hematology, Field of Applied Laboratory Science, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Osamu Hoshi
- Anatomy and Physiological Science, Field of Applied Laboratory Science, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Silvia Fischer
- Institute for Biochemistry, Medical Faculty, Justus-Liebig-Universität, Giessen, Germany
| | - Klaus T. Preissner
- Institute for Biochemistry, Medical Faculty, Justus-Liebig-Universität, Giessen, Germany
| | - Takatoshi Koyama
- Laboratory Molecular Genetics of Hematology, Field of Applied Laboratory Science, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- * E-mail:
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48
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Lutz S, Williams E, Muthu P. Engineering Therapeutic Enzymes. DIRECTED ENZYME EVOLUTION: ADVANCES AND APPLICATIONS 2017:17-67. [DOI: 10.1007/978-3-319-50413-1_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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49
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D'Avino C, Palmieri D, Braddom A, Zanesi N, James C, Cole S, Salvatore F, Croce CM, De Lorenzo C. A novel fully human anti-NCL immunoRNase for triple-negative breast cancer therapy. Oncotarget 2016; 7:87016-87030. [PMID: 27894092 PMCID: PMC5349967 DOI: 10.18632/oncotarget.13522] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 10/10/2016] [Indexed: 12/25/2022] Open
Abstract
Breast cancer is the most common cancer in women worldwide. A new promising anti-cancer therapy involves the use of monoclonal antibodies specific for target tumor-associated antigens (TAAs). A TAA of interest for immunotherapy of Triple Negative Breast Cancer (TNBC) is nucleolin (NCL), a multifunctional protein, selectively expressed on the surface of cancer cells, which regulates the biogenesis of specific microRNAs (miRNAs) involved in tumor development and drug-resistance. We previously isolated a novel human anti-NCL scFv, called 4LB5, that is endowed with selective anti-tumor effects. Here we report the construction and characterization of a novel immunoRNase constituted by 4LB5 and a human pancreatic RNase (HP-RNase) called "4LB5-HP-RNase". This immunoRNase retains both the enzymatic activity of human pancreatic RNase and the specific binding of the parental scFv to a panel of surface NCL-positive breast cancer cells. Notably, 4LB5-HP-RNase dramatically and selectively reduced the viability and proliferation of NCL-positive tumor cells in vitro and in vivo. Specifically, it induced apoptosis and reduced the levels of the tumorigenic miRNAs miR-21, -221 and -222. Thus, this novel immunoagent could be a valuable tool for the treatment of TNBC patients ineligible for currently available targeted treatments.
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Affiliation(s)
- Chiara D'Avino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy
- Ceinge Advanced Biotechnology S.C.ar.l., 80145 Naples, Italy
| | - Dario Palmieri
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, 43210 Ohio, USA
| | - Ashley Braddom
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, 43210 Ohio, USA
| | - Nicola Zanesi
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, 43210 Ohio, USA
| | - Cindy James
- Department of Mass Spectroscopy and Proteomics, The Ohio State University, Columbus, 43210 Ohio, USA
| | - Sara Cole
- Campus Microscopy and Imaging Facility, The Ohio State University, Columbus, 43210 Ohio, USA
| | | | - Carlo M. Croce
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, 43210 Ohio, USA
| | - Claudia De Lorenzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy
- Ceinge Advanced Biotechnology S.C.ar.l., 80145 Naples, Italy
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50
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Simões ICM, Costa IPD, Coimbra JTS, Ramos MJ, Fernandes PA. New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces. J Chem Inf Model 2016; 57:60-72. [DOI: 10.1021/acs.jcim.6b00378] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Inês C. M. Simões
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Inês P. D. Costa
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - João T. S. Coimbra
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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