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Kravchenko A, de Vries SJ, Smaïl-Tabbone M, Chauvot de Beauchene I. HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses. BMC Bioinformatics 2024; 25:129. [PMID: 38532339 DOI: 10.1186/s12859-024-05733-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND The RNA-Recognition motif (RRM) is a protein domain that binds single-stranded RNA (ssRNA) and is present in as much as 2% of the human genome. Despite this important role in biology, RRM-ssRNA interactions are very challenging to study on the structural level because of the remarkable flexibility of ssRNA. In the absence of atomic-level experimental data, the only method able to predict the 3D structure of protein-ssRNA complexes with any degree of accuracy is ssRNA'TTRACT, an ssRNA fragment-based docking approach using ATTRACT. However, since ATTRACT parameters are not ssRNA-specific and were determined in 2010, there is substantial opportunity for enhancement. RESULTS Here we present HIPPO, a composite RRM-ssRNA scoring potential derived analytically from contact frequencies in near-native versus non-native docking models. HIPPO consists of a consensus of four distinct potentials, each extracted from a distinct reference pool of protein-trinucleotide docking decoys. To score a docking pose with one potential, for each pair of RNA-protein coarse-grained bead types, each contact is awarded or penalised according to the relative frequencies of this contact distance range among the correct and incorrect poses of the reference pool. Validated on a fragment-based docking benchmark of 57 experimentally solved RRM-ssRNA complexes, HIPPO achieved a threefold or higher enrichment for half of the fragments, versus only a quarter with the ATTRACT scoring function. In particular, HIPPO drastically improved the chance of very high enrichment (12-fold or higher), a scenario where the incremental modelling of entire ssRNA chains from fragments becomes viable. However, for the latter result, more research is needed to make it directly practically applicable. Regardless, our approach already improves upon the state of the art in RRM-ssRNA modelling and is in principle extendable to other types of protein-nucleic acid interactions.
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Affiliation(s)
- Anna Kravchenko
- Université de Lorraine, CNRS, Inria, LORIA, 54000, Nancy, France
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Pangeni S, Biswas G, Kaushik V, Kuppa S, Yang O, Lin CT, Mishra G, Levy Y, Antony E, Ha T. Rapid Long-distance Migration of RPA on Single Stranded DNA Occurs Through Intersegmental Transfer Utilizing Multivalent Interactions. J Mol Biol 2024; 436:168491. [PMID: 38360091 PMCID: PMC10949852 DOI: 10.1016/j.jmb.2024.168491] [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: 12/28/2023] [Revised: 02/04/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Replication Protein A (RPA) is asingle strandedDNA(ssDNA)binding protein that coordinates diverse DNA metabolic processes including DNA replication, repair, and recombination. RPA is a heterotrimeric protein with six functional oligosaccharide/oligonucleotide (OB) domains and flexible linkers. Flexibility enables RPA to adopt multiple configurations andis thought to modulate its function. Here, usingsingle moleculeconfocal fluorescencemicroscopy combinedwith optical tweezers and coarse-grained molecular dynamics simulations, we investigated the diffusional migration of single RPA molecules on ssDNA undertension.The diffusioncoefficientDis the highest (20,000nucleotides2/s) at 3pNtension and in 100 mMKCl and markedly decreases whentensionor salt concentrationincreases. We attribute the tension effect to intersegmental transfer which is hindered by DNA stretching and the salt effect to an increase in binding site size and interaction energy of RPA-ssDNA. Our integrative study allowed us to estimate the size and frequency of intersegmental transfer events that occur through transient bridging of distant sites on DNA by multiple binding sites on RPA. Interestingly, deletion of RPA trimeric core still allowed significant ssDNA binding although the reduced contact area made RPA 15-fold more mobile. Finally, we characterized the effect of RPA crowding on RPA migration. These findings reveal how the high affinity RPA-ssDNA interactions are remodeled to yield access, a key step in several DNA metabolic processes.
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Affiliation(s)
- Sushil Pangeni
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Gargi Biswas
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, USA
| | - Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, USA
| | - Olivia Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chang-Ting Lin
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Garima Mishra
- Department of Physics, Ashoka University, Sonepet, Haryana, India
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, USA.
| | - Taekjip Ha
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA.
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Wang Y, Meng FL, Yeap LS. DNA flexibility can shape the preferential hypermutation of antibody genes. Trends Immunol 2024; 45:167-176. [PMID: 38402044 DOI: 10.1016/j.it.2024.01.005] [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: 12/28/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/26/2024]
Abstract
Antibody-coding genes accumulate somatic mutations to achieve antibody affinity maturation. Genetic dissection using various mouse models has shown that intrinsic hypermutations occur preferentially and are predisposed in the DNA region encoding antigen-contacting residues. The molecular basis of nonrandom/preferential mutations is a long-sought question in the field. Here, we summarize recent findings on how single-strand (ss)DNA flexibility facilitates activation-induced cytidine deaminase (AID) activity and fine-tunes the mutation rates at a mesoscale within the antibody variable domain exon. We propose that antibody coding sequences are selected based on mutability during the evolution of adaptive immunity and that DNA mechanics play a noncoding role in the genome. The mechanics code may also determine other cellular DNA metabolism processes, which awaits future investigation.
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Affiliation(s)
- Yanyan Wang
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fei-Long Meng
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Schiopu I, Dragomir I, Asandei A. Single molecule technique unveils the role of electrostatic interactions in ssDNA-gp32 molecular complex stability. RSC Adv 2024; 14:5449-5460. [PMID: 38352678 PMCID: PMC10862658 DOI: 10.1039/d3ra07746b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
The exploration of single-strand DNA-binding protein (SSB)-ssDNA interactions and their crucial roles in essential biological processes lagged behind other types of protein-nucleic acid interactions, such as protein-dsDNA and protein-RNA interactions. The ssDNA binding protein gene product 32 (gp32) of the T4 bacteriophage is a central integrating component of the replication complex that must continuously bind to and unbind from transiently exposed template strands during the DNA synthesis. To gain deeper insights into the electrostatic conditions influencing the stability of the ssDNA-gp32 molecular complex, like the salt concentration or some metal ions proven to specifically bind to gp32, we employed a method that performs rapid measurements of the DNA-protein stability using an α-Hemolysin (α-HL) protein nanopore. We indirectly probed the stability of a protein-nucleic acid complex by monitoring the dissociation process between the gp32 protein and the ssDNA molecular complex in single-molecular electrophysiology experiments, but also through fluorescence spectroscopy techniques. We have shown that the complex is more stable in 0.5 M KCl solution than in 2 M KCl solution and that the presence of Zn2+ ions further increases this stability for any salt used in the present study. This method can be applied to other nucleic acid-protein molecular complexes, as well as for an accurate determination of the drug-protein carrier stability.
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Affiliation(s)
- Irina Schiopu
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
| | - Isabela Dragomir
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
| | - Alina Asandei
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
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Collins MS, Imbrogno MA, Kopras EJ, Howard JA, Zhang N, Kramer EL, Hudock KM. Heterogeneity in Neutrophil Extracellular Traps from Healthy Human Subjects. Int J Mol Sci 2023; 25:525. [PMID: 38203698 PMCID: PMC10779146 DOI: 10.3390/ijms25010525] [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: 10/01/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Neutrophil extracellular traps (NETs), a key component of early defense against microbial infection, are also associated with tissue injury. NET composition has been reported to vary with some disease states, but the composition and variability of NETs across many healthy subjects provide a critical comparison that has not been well investigated. We evaluated NETs from twelve healthy subjects of varying ages isolated from multiple blood draws over a three-and-one-half-year period to delineate the variability in extracellular DNA, protein, enzymatic activities, and susceptibility to protease inhibitors. We calculated correlations for NET constituents and loss of human bronchial epithelial barrier integrity, measured by transepithelial electrical resistance, after NET exposure. We found that although there was some variability within the same subject over time, the mean NET total DNA, dsDNA, protein, LDH, neutrophil elastase (NE), and proteinase 3 (PR3) in isolated NETs were consistent across subjects. NET serine protease activity varied considerably within the same donor from day to day. The mean NET cathepsin G and MPO were significantly different across donors. IL-8 > IL-1RA > G-CSF were the most abundant cytokines in NETs. There was no significant difference in the mean concentration or variability of IL-8, IL-1RA, G-CSF, IL-1α, IL-1β, or TNF-α in different subjects' NETs. NET DNA concentration was correlated with increased NET neutrophil elastase activity and higher NET IL-1RA concentrations. The mean reduction in protease activity by protease inhibitors was significantly different across donors. NET DNA concentration correlated best with reductions in the barrier integrity of human bronchial epithelia. Defining NET concentration by DNA content correlates with other NET components and reductions in NET-driven epithelial barrier dysfunction, suggesting DNA is a reasonable surrogate measurement for these complex structures in healthy subjects.
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Affiliation(s)
- Margaret S. Collins
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Michelle A. Imbrogno
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Elizabeth J. Kopras
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - James A. Howard
- Department of Pharmacology & Systems Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Nanhua Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Elizabeth L. Kramer
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Division of Pediatric Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kristin M. Hudock
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
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Sharma PV, Jain S, Sen R. Peptides designed from a bacteriophage capsid protein function as synthetic transcription repressors. J Biol Chem 2023; 299:105373. [PMID: 37865318 PMCID: PMC10692717 DOI: 10.1016/j.jbc.2023.105373] [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: 07/09/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023] Open
Abstract
The bacteriophage capsid protein, Psu (polarity suppression), inhibits the bacterial transcription terminator, Rho. In an effort to find nontraditional antibacterial agents, we previously designed peptides from the Psu C terminus that function as inhibitors of Rho. Here, we demonstrated that these peptides have positive surface-charge densities, and they downregulate many genes in Escherichia coli. We hypothesized that these peptides could bind to nucleic acids and repress gene expression. One of these peptides, peptide 33, represses in vitro transcription from the T7A1 and Plac promoters efficiently by blocking the access of RNA polymerase to the promoter, a mode of transcription repression akin to many bacterial repressors. In vivo, expressions of the peptides reduce the total RNA level as well as transcription from Plac and Posm promoters significantly. However, they are less efficient in repressing transcription from the rRNA promoters with a very high turnover of RNA polymerase. The peptide 33 binds to both single and dsDNA as well as to RNA with dissociation constants ranging from 1 to 5 μM exhibiting preferences for the single-stranded DNA and RNAs. These interactions are salt-resistant and not sequence-specific. Interactions with dsDNA are entropy-driven, while it is enthalpy-driven for the ssDNA. This mode of interaction with nucleic acids is similar to many nonspecific ssDNA-binding proteins. Expression of peptide 33 induces cell elongation and impaired cell division, possibly due to the dislodging of the DNA-binding proteins. Overall, we surmised that these synthetic transcription repressors would function like bacterial nucleoid-associated proteins.
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Affiliation(s)
- Pankaj V Sharma
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Hyderabad, India; Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sriyans Jain
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ranjan Sen
- Laboratory of Transcription, Center for DNA Fingerprinting and Diagnostics, Hyderabad, India.
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Collins MS, Imbrogno MA, Kopras EJ, Howard JA, Zhang N, Kramer EL, Hudock KM. Heterogeneity in Neutrophil Extracellular Traps from Healthy Human Subjects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565547. [PMID: 37961496 PMCID: PMC10635125 DOI: 10.1101/2023.11.03.565547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Neutrophil Extracellular Traps (NETs), a key component of early defense against microbial infection, are also associated with tissue injury. NET composition has been reported to vary with some disease states, but the composition and variability of NETs across many healthy subjects provides a critical comparison that has not been well investigated. We evaluated NETs from twelve healthy subjects of varying ages isolated from multiple blood draws over a three and one half-year period to delineate the variability in extracellular DNA, protein, enzymatic activities, and susceptibility to protease inhibitors. We calculated correlations for NET constituents and loss of human bronchial epithelial barrier integrity, measured by transepithelial electrical resistance, after NET exposure. We found that although there was some variability within the same subject over time, the mean numbers of neutrophils, protein, LDH, serine protease activities, and cytokines IL-8, IL-1RA, and G-CSF in isolated NETs were consistent across subjects. Total DNA and double stranded DNA content in NETs were different across donors. NETs had little or no TNFα, IL-17A, or GM-CSF. NET DNA concentration correlated with increased NET neutrophil elastase activity and higher NET IL-1RA concentrations. NET serine protease activity varied considerably within the same donor from day-to-day. Mean response to protease inhibitors was significantly different across donors. NET DNA concentration correlated best with reductions in barrier integrity of human bronchial epithelia. Defining NET concentration by DNA content correlates with other NET components and reductions in NET-driven epithelial barrier dysfunction, suggesting DNA is a reasonable surrogate measurement for these complex structures in healthy subjects.
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Affiliation(s)
- Margaret S. Collins
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Michelle A. Imbrogno
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Elizabeth J. Kopras
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - James A. Howard
- Department of Pharmacology & Systems Physiology, University of Cincinnati, Cincinnati, OH, USA
| | - Nanhua Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Elizabeth L. Kramer
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
- Division of Pediatric Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Kristin M. Hudock
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
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8
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Jain A, Begum T, Ahmad S. Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates. J Mol Biol 2023; 435:168208. [PMID: 37479078 DOI: 10.1016/j.jmb.2023.168208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/20/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Identification of key sequence, expression and function related features of nucleic acid-sensing host proteins is of fundamental importance to understand the dynamics of pathogen-specific host responses. To meet this objective, we considered toll-like receptors (TLRs), a representative class of membrane-bound sensor proteins, from 17 vertebrate species covering mammals, birds, reptiles, amphibians, and fishes in this comparative study. We identified the molecular signatures of host TLRs that are responsible for sensing pathogen nucleic acids or other pathogen-associated molecular patterns (PAMPs), and potentially play important roles in host defence mechanism. Interestingly, our findings reveal that such host-specific features are directly related to the strand (single or double) specificity of nucleic acid from pathogens. However, during host-pathogen interactions, such features were unable to explain the pathogenic PAMP (i.e., DNA, RNA or other) selectivity, suggesting a more complex mechanism. Using these features, we developed a number of machine learning models, of which Random Forest achieved a high performance (94.57% accuracy) to predict strand specificity of TLRs from protein-derived features. We applied the trained model to propose strand specificity of some previously uncharacterized distinct fish-specific novel TLRs (TLR18, TLR23, TLR24, TLR25, TLR27).
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Affiliation(s)
- Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India. https://twitter.com/@Anuja334
| | - Tina Begum
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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Aminu S, Danazumi AU, Alhafiz ZA, Gorna MW, Ibrahim MA. β-Sitosterol could serve as a dual inhibitor of Trypanosoma congolense sialidase and phospholipase A 2: in vitro kinetic analyses and molecular dynamic simulations. Mol Divers 2023; 27:1645-1660. [PMID: 36042119 DOI: 10.1007/s11030-022-10517-2] [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: 06/10/2022] [Accepted: 08/15/2022] [Indexed: 11/24/2022]
Abstract
The involvement of Trypanosoma congolense sialidase alongside phospholipase A2 has been widely accepted as the major contributing factor to anemia during African animal trypanosomiasis. The enzymes aid the parasite in scavenging sialic acid and fatty acids necessary for survival in the infected host, but there are no specific drug candidates against the two enzymes. This study investigated the inhibitory effects of β-sitosterol on the partially purified T. congolense sialidase and phospholipase A2. Purification of the enzymes using DEAE cellulose column led to fractions with highest specific activities of 8016.41 and 39.26 µmol/min/mg for sialidase and phospholipase A2, respectively. Inhibition kinetics studies showed that β-sitosterol is non-competitive and an uncompetitive inhibitor of sialidase and phospholipase A2 with inhibition binding constants of 0.368 and 0.549 µM, respectively. Molecular docking of the compound revealed binding energies of - 8.0 and - 8.6 kcal/mol against the sialidase and phospholipase A2, respectively. Furthermore, 100 ns molecular dynamics simulation using GROMACS revealed stable interaction of β-sitosterol with both enzymes. Hydrogen bond interactions between the ligand and Glu284 and Leu102 residues of the sialidase and phospholipase A2, respectively, were found to be the major stabilizing forces. In conclusion, β-sitosterol could serve as a dual inhibitor of T. congolense sialidase and phospholipase A2; hence, the compound could be exploited further in the search for newer trypanocides.
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Affiliation(s)
- Suleiman Aminu
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Ammar Usman Danazumi
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Zainab Aliyu Alhafiz
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
- Department of Biochemistry, Federal University, Gusau, Nigeria
| | - Maria Wiktoria Gorna
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, Warsaw, Poland
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Acquah FA, Mooers BHM. Targeting RNA Structure to Inhibit Editing in Trypanosomes. Int J Mol Sci 2023; 24:10110. [PMID: 37373258 PMCID: PMC10298474 DOI: 10.3390/ijms241210110] [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: 05/01/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Mitochondrial RNA editing in trypanosomes represents an attractive target for developing safer and more efficient drugs for treating infections with trypanosomes because this RNA editing pathway is not found in humans. Other workers have targeted several enzymes in this editing system, but not the RNA. Here, we target a universal domain of the RNA editing substrate, which is the U-helix formed between the oligo-U tail of the guide RNA and the target mRNA. We selected a part of the U-helix that is rich in G-U wobble base pairs as the target site for the virtual screening of 262,000 compounds. After chemoinformatic filtering of the top 5000 leads, we subjected 50 representative complexes to 50 nanoseconds of molecular dynamics simulations. We identified 15 compounds that retained stable interactions in the deep groove of the U-helix. The microscale thermophoresis binding experiments on these five compounds show low-micromolar to nanomolar binding affinities. The UV melting studies show an increase in the melting temperatures of the U-helix upon binding by each compound. These five compounds can serve as leads for drug development and as research tools to probe the role of the RNA structure in trypanosomal RNA editing.
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Affiliation(s)
- Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Laboratory of Biomolecular Structure and Function, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Zhao R, Fang X, Mai Z, Chen X, Mo J, Lin Y, Xiao R, Bao X, Weng X, Zhou X. Transcriptome-wide identification of single-stranded RNA binding proteins. Chem Sci 2023; 14:4038-4047. [PMID: 37063799 PMCID: PMC10094363 DOI: 10.1039/d3sc00957b] [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: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 04/18/2023] Open
Abstract
RNA-protein interactions are precisely regulated by RNA secondary structures in various biological processes. Large-scale identification of proteins that interact with particular RNA structure is important to the RBPome. Herein, a kethoxal assisted single-stranded RNA interactome capture (KASRIC) strategy was developed to globally identify single-stranded RNA binding proteins (ssRBPs). This approach combines RNA secondary structure probing technology with the conventional method of RNA-binding proteins profiling, realizing the transcriptome-wide identification of ssRBPs. Applying KASRIC, we identified 3180 candidate RBPs and 244 candidate ssRBPs in HeLa cells. Importantly, the 244 candidate ssRBPs contained 55 previously reported ssRBPs and 189 novel ssRBPs. Function analysis of the candidate ssRBPs exhibited enrichment in cellular processes related to RNA splicing and RNA degradation. The KASRIC strategy will facilitate the investigation of RNA-protein interactions.
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Affiliation(s)
- Ruiqi Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Xin Fang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Zhibiao Mai
- Laboratory of RNA Molecular Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences Guangzhou Guangdong Province 510530 China
| | - Xi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Jing Mo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Yingying Lin
- Laboratory of RNA Molecular Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences Guangzhou Guangdong Province 510530 China
| | - Rui Xiao
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University Wuhan Hubei 430071 China
- TaiKang Center for Life and Medical Sciences, Wuhan University Wuhan Hubei 430071 China
| | - Xichen Bao
- Laboratory of RNA Molecular Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences Guangzhou Guangdong Province 510530 China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University Wuhan Hubei 430072 P. R. China
- TaiKang Center for Life and Medical Sciences, Wuhan University Wuhan Hubei 430071 China
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12
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McGregor LA, Zhu B, Goetz AM, Sczepanski JT. Thymine DNA Glycosylase is an RNA-Binding Protein with High Selectivity for G-Rich Sequences. J Biol Chem 2023; 299:104590. [PMID: 36889585 PMCID: PMC10124917 DOI: 10.1016/j.jbc.2023.104590] [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: 12/28/2022] [Revised: 02/17/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
Thymine DNA glycosylase (TDG) is a multifaceted enzyme involved in several critical biological pathways, including transcriptional activation, DNA demethylation, and DNA repair. Recent studies have established regulatory relationships between TDG and RNA, but the molecular interactions underlying these relationships is poorly understood. Herein, we now demonstrate that TDG binds directly to RNA with nanomolar affinity. Using synthetic oligonucleotides of defined length and sequence, we show that TDG has a strong preference for binding G-rich sequences in single-stranded RNA but binds weakly to single-stranded DNA and duplex RNA. TDG also binds tightly to endogenous RNA sequences. Studies with truncated proteins indicate that TDG binds RNA primarily through its structured catalytic domain and that its disordered C-terminal domain plays a key role in regulating TDG's affinity and selectivity for RNA. Finally, we show that RNA competes with DNA for binding to TDG, resulting in inhibition of TDG-mediated excision in the presence of RNA. Together, this work provides support for and insights into a mechanism wherein TDG-mediated processes (e.g., DNA demethylation) are regulated through the direct interactions of TDG with RNA.
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Affiliation(s)
- Lauren A McGregor
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, USA
| | - Baiyu Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, USA
| | - Allison M Goetz
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, USA
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13
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Bai M, Liu ZL, Zhou YY, Xu QX, Liu TX, Tian HG. Influence of diverse storage conditions of double-stranded RNA in vitro on the RNA interference efficiency in vivo insect Tribolium castaneum. PEST MANAGEMENT SCIENCE 2023; 79:45-54. [PMID: 36086883 DOI: 10.1002/ps.7171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/10/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND A significant variation in RNA interference (RNAi) efficiency hinders further functional gene studies and pest control application in many insects. The available double-stranded RNA (dsRNA) molecules introduced into the target cells are regarded as the crucial factor for efficient RNAi response. However, numerous studies have only focused on dsRNA stability in vivo; it is uncertain whether different dsRNA storage conditions in vitro play a role in variable RNAi efficiency among insects. RESULTS A marker gene cardinal, which leads to white eyes when knocked-down in the red flour beetle Tribolium castaneum, was used to evaluate the effects of RNAi efficiency under different dsRNA storage conditions. We demonstrated that the dsRNA molecule is very stable under typical cryopreservation temperatures (-80 and -20 °C) within 180 days, and RNAi efficiency shows no significant differences under either low temperature. Unexpectedly, while dsRNA molecules were treated with multiple freeze-thaw cycles up to 50 times between -80/-20 °C and room temperature, we discovered that dsRNA integrity and RNAi efficiency were comparable with fresh dsRNA. Finally, when the stability of dsRNA was further measured under refrigerated storage conditions (4 °C), we surprisingly found that dsRNA is still stable within 180 days and can induce an efficient RNAi response as that of initial dsRNA. CONCLUSION Our results indicate that dsRNA is extraordinarily stable under various temperature storage conditions that did not significantly impact RNAi efficiency in vivo insects. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Mei Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
- Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Zi-Ling Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
- Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yu-Yu Zhou
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
- Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Qiu-Xuan Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
- Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Tong-Xian Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
- Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Hong-Gang Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
- Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, China
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14
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Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA. PLoS One 2023; 18:e0278396. [PMID: 36656834 PMCID: PMC9851514 DOI: 10.1371/journal.pone.0278396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 11/15/2022] [Indexed: 01/20/2023] Open
Abstract
Human Replication Protein A (hRPA) is a multidomain protein that interacts with ssDNA intermediates to provide the latter much-needed stability during DNA metabolism and maintain genomic integrity. Although the ssDNA organization with hRPA was studied recently through experimental means, characterizing the underlying mechanism at the atomic level remains challenging because of the dynamic domain architecture of hRPA and poorly understood heterogeneity of ssDNA-protein interactions. Here, we used a computational framework, precisely tailored to capture protein-ssDNA interactions, and investigated the binding of hRPA with a 60 nt ssDNA. Two distinct binding mechanisms are realized based on the hRPA domain flexibility. For a rigid domain architecture of hRPA, ssDNA binds sequentially with hRPA domains, resulting in slow association kinetics. The binding pathway involves the formation of stable and distinct intermediate states. On contrary, for a flexible domain architecture of hRPA, ssDNA binds synergistically to the A and B domains followed by the rest of hRPA. The domain dynamics in hRPA alleviates the free energy cost of domain orientation necessary for specific binding with ssDNA, leading to fast association kinetics along a downhill binding free energy landscape. An ensemble of free energetically degenerate intermediate states is encountered that makes it arduous to characterize them structurally. An excellent match between our results with the available experimental observations provides new insights into the rich dynamics of hRPA binding to ssDNA and in general paves the way to investigate intricate details of ssDNA-protein interactions, crucial for cellular functioning.
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15
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Serrano JC, von Trentini D, Berríos KN, Barka A, Dmochowski IJ, Kohli RM. Structure-Guided Design of a Potent and Specific Inhibitor against the Genomic Mutator APOBEC3A. ACS Chem Biol 2022; 17:3379-3388. [PMID: 36475588 PMCID: PMC9990883 DOI: 10.1021/acschembio.2c00796] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleic acid structure plays a critical role in governing the selectivity of DNA- and RNA-modifying enzymes. In the case of the APOBEC3 family of cytidine deaminases, these enzymes catalyze the conversion of cytosine (C) to uracil (U) in single-stranded DNA, primarily in the context of innate immunity. DNA deamination can also have pathological consequences, accelerating the evolution of viral genomes or, when the host genome is targeted by either APOBEC3A (A3A) or APOBEC3B (A3B), promoting tumor evolution leading to worse patient prognosis and chemotherapeutic resistance. For A3A, nucleic acid secondary structure has emerged as a critical determinant of substrate targeting, with a predilection for DNA that can form stem loop hairpins. Here, we report the development of a specific nanomolar-level, nucleic acid-based inhibitor of A3A. Our strategy relies on embedding the nucleobase 5-methylzebularine, a mechanism-based inhibitor, into a DNA dumbbell structure, which mimics the ideal substrate secondary structure for A3A. Structure-activity relationship studies using a panel of diverse inhibitors reveal a critical role for the stem and position of the inhibitor moiety in achieving potent inhibition. Moreover, we demonstrate that DNA dumbbell inhibitors, but not nonstructured inhibitors, show specificity against A3A relative to the closely related catalytic domain of A3B. Overall, our work demonstrates the feasibility of leveraging secondary structural preferences in inhibitor design, offering a blueprint for further development of modulators of DNA-modifying enzymes and potential therapeutics to circumvent APOBEC-driven viral and tumor evolution.
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Affiliation(s)
- Juan C. Serrano
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Dora von Trentini
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Kiara N. Berríos
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Aleksia Barka
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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16
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Krepl M, Pokorná P, Mlýnský V, Stadlbauer P, Šponer J. Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field. Nucleic Acids Res 2022; 50:12480-12496. [PMID: 36454011 PMCID: PMC9757038 DOI: 10.1093/nar/gkac1106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022] Open
Abstract
Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein-RNA interactions. Many such complexes were characterized using nuclear magnetic resonance (NMR) and/or X-ray crystallography techniques, revealing ensemble-averaged pictures of the bound states. However, it is becoming widely accepted that better understanding of protein-RNA interactions would be obtained from ensemble descriptions. Indeed, earlier molecular dynamics simulations of bound states indicated visible dynamics at the RNA-RRM interfaces. Here, we report the first atomistic simulation study of spontaneous binding of short RNA sequences to RRM domains of HuR and SRSF1 proteins. Using a millisecond-scale aggregate ensemble of unbiased simulations, we were able to observe a few dozen binding events. HuR RRM3 utilizes a pre-binding state to navigate the RNA sequence to its partially disordered bound state and then to dynamically scan its different binding registers. SRSF1 RRM2 binding is more straightforward but still multiple-pathway. The present study necessitated development of a goal-specific force field modification, scaling down the intramolecular van der Waals interactions of the RNA which also improves description of the RNA-RRM bound state. Our study opens up a new avenue for large-scale atomistic investigations of binding landscapes of protein-RNA complexes, and future perspectives of such research are discussed.
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Affiliation(s)
| | - Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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17
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Sarli SL, Watts JK. Harnessing nucleic acid technologies for human health on earth and in space. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:113-126. [PMID: 36336357 DOI: 10.1016/j.lssr.2022.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Nucleic acid therapeutics are a versatile class of sequence-programmable drugs that offer a robust and clinically viable strategy to modulate expression or correct genetic defects contributing to disease. The majority of drugs currently on the market target proteins; however, proteins only represent a subset of possible disease targets. Nucleic acid therapeutics allow intuitive engagement with genome sequences providing a more direct way to target many diseases at their genetic root cause. Their clinical success depends on platform technologies which can support durable and well tolerated pharmacological activity in a given tissue. Nucleic acid drugs possess a potent combination of target specificity and adaptability required to advance drug development for many diseases. As these therapeutic technologies mature, their clinical applications can also expand access to personalized therapies for patients with rare or solo genetic diseases. Spaceflight crew members exposed to the unique hazards of spaceflight, especially those related to galactic cosmic radiation (GCR) exposure, represent another patient subset who may also benefit from nucleic acid drugs as countermeasures. In this review, we will discuss the various classes of RNA- and DNA-targeted nucleic acid drugs, provide an overview of their present-day clinical applications, and describe major strategies to improve their delivery, safety, and overall efficacy.
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Affiliation(s)
- Samantha L Sarli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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18
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Kurup HM, Kvach MV, Harjes S, Barzak FM, Jameson GB, Harjes E, Filichev VV. Design, Synthesis, and Evaluation of a Cross-Linked Oligonucleotide as the First Nanomolar Inhibitor of APOBEC3A. Biochemistry 2022; 61:2568-2578. [DOI: 10.1021/acs.biochem.2c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Harikrishnan M. Kurup
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Maksim V. Kvach
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Stefan Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Fareeda M. Barzak
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Geoffrey B. Jameson
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V. Filichev
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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19
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Szczuka A, Horton J, Evans KJ, DiPietri VT, Sivey JD, Wigginton KR. Chloride Enhances DNA Reactivity with Chlorine under Conditions Relevant to Water Treatment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13347-13356. [PMID: 36027047 PMCID: PMC9494735 DOI: 10.1021/acs.est.2c03267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Free available chlorine (FAC) is widely used to inactivate viruses by oxidizing viral components, including genomes. It is commonly assumed that hypochlorous acid (HOCl) is the chlorinating agent responsible for virus inactivation; however, recent studies have underscored that minor constituents of FAC existing in equilibrium with HOCl, such as molecular chlorine (Cl2), can influence FAC reactivity toward select organic compounds. This study measures the FAC reaction kinetics with dsDNA and ssDNA extracted from representative bacteriophages (T3 and ϕX174) in samples augmented with chloride. Herein, chloride enhances FAC reactivity toward dsDNA and, to a lesser extent, toward ssDNA, especially at pH < 7.5. The enhanced reactivity can be attributed to the formation of Cl2. Second-order rate constants were determined for reactions of ssDNA and dsDNA with HOCl and Cl2. DNA chlorination kinetics followed the reactivity-selectivity principle, where the more-reactive nucleophilic species (ssDNA, ∼100× more reactive than dsDNA) reacted less selectively with electrophilic FAC species. The addition of chloride was also shown to enhance the inactivation of bacteriophage T3 (dsDNA genome) by FAC but did not enhance the inactivation of bacteriophage ϕX174 (ssDNA genome). Overall, the results suggest that Cl2 is an important chlorinating agent of nucleic acids and viruses.
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Affiliation(s)
- Aleksandra Szczuka
- Department
of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jordon Horton
- Department
of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kelsey J. Evans
- Department
of Chemistry, Towson University, Towson, Maryland 21252, United States
| | - Vincent T. DiPietri
- Department
of Chemistry, Towson University, Towson, Maryland 21252, United States
| | - John D. Sivey
- Department
of Chemistry, Towson University, Towson, Maryland 21252, United States
| | - Krista R. Wigginton
- Department
of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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20
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Anindita PD, Halbeisen M, Řeha D, Tuma R, Franta Z. Mechanistic insight into the RNA stimulated-ATPase activity of tick-borne encephalitis virus helicase. J Biol Chem 2022; 298:102383. [PMID: 35987382 PMCID: PMC9490040 DOI: 10.1016/j.jbc.2022.102383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/05/2022] Open
Abstract
The helicase domain of nonstructural protein 3 (NS3H) unwinds the double-stranded RNA replication intermediate in an ATP-dependent manner during the flavivirus life cycle. While the ATP hydrolysis mechanism of Dengue and Zika viruses NS3H has been extensively studied, little is known in the case of the tick-borne encephalitis virus NS3H. We demonstrate that ssRNA binds with nanomolar affinity to NS3H and strongly stimulates the ATP hydrolysis cycle, whereas ssDNA binds only weakly and inhibits ATPase activity in a noncompetitive manner. Thus, NS3H is an RNA-specific helicase, whereas DNA might act as an allosteric inhibitor. Using modeling, we explored plausible allosteric mechanisms by which ssDNA inhibits the ATPase via nonspecific binding in the vicinity of the active site and ATP repositioning. We captured several structural snapshots of key ATP hydrolysis stages using X-ray crystallography. One intermediate, in which the inorganic phosphate and ADP remained trapped inside the ATPase site after hydrolysis, suggests that inorganic phosphate release is the rate-limiting step. Using structure-guided modeling and molecular dynamics simulation, we identified putative RNA-binding residues and observed that the opening and closing of the ATP-binding site modulates RNA affinity. Site-directed mutagenesis of the conserved RNA-binding residues revealed that the allosteric activation of ATPase activity is primarily communicated via an arginine residue in domain 1. In summary, we characterized conformational changes associated with modulating RNA affinity and mapped allosteric communication between RNA-binding groove and ATPase site of tick-borne encephalitis virus helicase.
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Affiliation(s)
| | - Marco Halbeisen
- Department of Chemistry, Faculty of Science, University of South Bohemia, Czech Republic
| | - David Řeha
- Department of Chemistry, Faculty of Science, University of South Bohemia, Czech Republic
| | - Roman Tuma
- Department of Chemistry, Faculty of Science, University of South Bohemia, Czech Republic
| | - Zdenek Franta
- Department of Chemistry, Faculty of Science, University of South Bohemia, Czech Republic.
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21
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Pabbathi A, Coleman L, Godar S, Paul A, Garlapati A, Spencer M, Eller J, Alper JD. Long-range electrostatic interactions significantly modulate the affinity of dynein for microtubules. Biophys J 2022; 121:1715-1726. [PMID: 35346642 PMCID: PMC9117880 DOI: 10.1016/j.bpj.2022.03.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/13/2022] [Accepted: 03/24/2022] [Indexed: 11/02/2022] Open
Abstract
The dynein family of microtubule minus-end-directed motor proteins drives diverse functions in eukaryotic cells, including cell division, intracellular transport, and flagellar beating. Motor protein processivity, which characterizes how far a motor walks before detaching from its filament, depends on the interaction between its microtubule-binding domain (MTBD) and the microtubule. Dynein's MTBD switches between high- and low-binding affinity states as it steps. Significant structural and functional data show that specific salt bridges within the MTBD and between the MTBD and the microtubule govern these affinity state shifts. However, recent computational work suggests that nonspecific, long-range electrostatic interactions between the MTBD and the microtubule may also play an important role in the processivity of dynein. To investigate this hypothesis, we mutated negatively charged amino acids remote from the dynein MTBD-microtubule-binding interface to neutral residues and measured the binding affinity using microscale thermophoresis and optical tweezers. We found a significant increase in the binding affinity of the mutated MTBDs for microtubules. Furthermore, we found that charge screening by free ions in solution differentially affected the binding and unbinding rates of MTBDs to microtubules. Together, these results demonstrate a significant role for long-range electrostatic interactions in regulating dynein-microtubule affinity. Moreover, these results provide insight into the principles that potentially underlie the biophysical differences between molecular motors with various processivities and protein-protein interactions more generally.
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Affiliation(s)
- Ashok Pabbathi
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Lawrence Coleman
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Subash Godar
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Apurba Paul
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina; Eukaryotic Pathogen Innovations Center, Clemson, University, Clemson, South Carolina
| | - Aman Garlapati
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, South Carolina
| | - Matheu Spencer
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Jared Eller
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina; Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina
| | - Joshua Daniel Alper
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina; Eukaryotic Pathogen Innovations Center, Clemson, University, Clemson, South Carolina; Department of Biological Sciences, Clemson University, Clemson, South Carolina.
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22
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Maffeo C, Chou HY, Aksimentiev A. Single-molecule biophysics experiments in silico: Toward a physical model of a replisome. iScience 2022; 25:104264. [PMID: 35521518 PMCID: PMC9062759 DOI: 10.1016/j.isci.2022.104264] [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: 11/16/2021] [Revised: 03/23/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022] Open
Abstract
The interpretation of single-molecule experiments is frequently aided by computational modeling of biomolecular dynamics. The growth of computing power and ongoing validation of computational models suggest that it soon may be possible to replace some experiments outright with computational mimics. Here, we offer a blueprint for performing single-molecule studies in silico using a DNA-binding protein as a test bed. We demonstrate how atomistic simulations, typically limited to sub-millisecond durations and zeptoliter volumes, can guide development of a coarse-grained model for use in simulations that mimic single-molecule experiments. We apply the model to recapitulate, in silico, force-extension characterization of protein binding to single-stranded DNA and protein and DNA replacement assays, providing a detailed portrait of the underlying mechanics. Finally, we use the model to simulate the trombone loop of a replication fork, a large complex of proteins and DNA. Coarse-grained model derived from all-atom simulation recapitulates experiments Model reproduces the elastic response to force and exchange dynamics Model reveals structure of intermediate states usually inaccessible to experiment Model applied to viral replisome with trombone loop containing tens of SSB proteins
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Matthews Avenue, Urbana, 61801 IL, USA
| | - Han-Yi Chou
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Matthews Avenue, Urbana, 61801 IL, USA
- Corresponding author
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23
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Pant P, Pathak A, Jayaram B. Bicyclo-DNA mimics with enhanced protein binding affinities: insights from molecular dynamics simulations. J Biomol Struct Dyn 2022; 41:4040-4047. [PMID: 35403569 DOI: 10.1080/07391102.2022.2061594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA-protein interactions occur at all levels of DNA expression and replication and are crucial determinants for the survival of a cell. Several modified nucleotides have been utilized to manipulate these interactions and have implications in drug discovery. In the present article, we evaluated the binding of bicyclo-nucleotides (generated by forming a methylene bridge between C1' and C5' in sugar, leading to a bicyclo system with C2' axis of symmetry at the nucleotide level) to proteins. We utilized four ssDNA-protein complexes with experimentally known binding free energies and investigated the binding of modified nucleotides to proteins via all-atom explicit solvent molecular dynamics (MD) simulations (200 ns), and compared the binding with control ssDNA-protein systems. The modified ssDNA displayed enhanced binding to proteins as compared to the control ssDNA, as seen by means of MD simulations followed by MM-PBSA calculations. Further, the Delphi-based electrostatic estimation revealed that the high binding of modified ssDNA to protein might be related to the enhanced electrostatic complementarity displayed by the modified ssDNA molecules in all the four systems considered for the study. The improved binding achieved with modified nucleotides can be utilized to design and develop anticancer/antisense molecules capable of targeting proteins or ssRNAs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pradeep Pant
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi, India
| | - Amita Pathak
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi, India
| | - B Jayaram
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi, India.,Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
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24
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Evaluation of FRET X for single-molecule protein fingerprinting. iScience 2021; 24:103239. [PMID: 34729466 PMCID: PMC8546410 DOI: 10.1016/j.isci.2021.103239] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/03/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
Single-molecule protein identification is an unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands and accumulated FRET efficiencies constitute the fingerprint for a protein. To evaluate the feasibility of this approach, we simulated fingerprints for hundreds of proteins using a coarse-grained lattice model and experimentally demonstrated FRET X fingerprinting on model peptides. Measured fingerprints are in agreement with our simulations, corroborating the validity of our modeling approach. In a simulated complex mixture of >300 human proteins of which only cysteines, lysines, and arginines were labeled, a support vector machine was able to identify constituents with 95% accuracy. We anticipate that our FRET X fingerprinting approach will form the basis of an analysis tool for targeted proteomics. We propose a FRET-based single-molecule protein identification method Peptides are experimentally distinguishable by their fingerprints Our approach can classify the constituents of complex samples with 95% accuracy
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25
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Mias-Lucquin D, Chauvot de Beauchene I. Conformational variability in proteins bound to single-stranded DNA: A new benchmark for new docking perspectives. Proteins 2021; 90:625-631. [PMID: 34617336 PMCID: PMC9292434 DOI: 10.1002/prot.26258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 09/15/2021] [Accepted: 09/27/2021] [Indexed: 12/19/2022]
Abstract
We explored the Protein Data Bank (PDB) to collect protein-ssDNA structures and create a multi-conformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA unbound structure is included in the benchmark. For the 91 sequence-identity groups identified as bound-unbound structures of the same protein, we studied the conformational changes in the protein induced by the ssDNA binding. Moreover, based on several bound or unbound protein structures in some groups, we also assessed the intrinsic conformational variability in either bound or unbound conditions and compared it to the supposedly binding-induced modifications. To illustrate a use case of this benchmark, we performed docking experiments using ATTRACT docking software. This benchmark is, to our knowledge, the first one made to peruse available structures of ssDNA-protein interactions to such an extent, aiming to improve computational docking tools dedicated to this kind of molecular interactions.
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26
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Shao J, Yan Y, Ding D, Wang D, He Y, Pan Y, Yan W, Kharbanda A, Li H, Huang H. Destruction of DNA-Binding Proteins by Programmable Oligonucleotide PROTAC (O'PROTAC): Effective Targeting of LEF1 and ERG. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102555. [PMID: 34397171 PMCID: PMC8529430 DOI: 10.1002/advs.202102555] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/30/2021] [Indexed: 05/03/2023]
Abstract
DNA-binding proteins, including transcription factors (TFs), play essential roles in various cellular processes and pathogenesis of diseases, deeming to be potential therapeutic targets. However, these proteins are generally considered undruggable as they lack an enzymatic catalytic site or a ligand-binding pocket. Proteolysis-targeting chimera (PROTAC) technology has been developed by engineering a bifunctional molecule chimera to bring a protein of interest (POI) to the proximity of an E3 ubiquitin ligase, thus inducing the ubiquitination of POI and further degradation through the proteasome pathway. Here, the development of oligonucleotide-based PROTAC (O'PROTACs), a class of noncanonical PROTACs in which a TF-recognizing double-stranded oligonucleotide is incorporated as a binding moiety of POI is reported. It is demonstrated that O'PROTACs of lymphoid enhancer-binding factor 1 (LEF1) and ETS-related gene (ERG), two highly cancer-related transcription factors, successfully promote degradation of these proteins, impede their transcriptional activity, and inhibit cancer cell growth in vitro and in vivo. The programmable nature of O'PROTACs indicates that this approach is also applicable to destruct other TFs. O'PROTACs not only can serve as a research tool but also can be harnessed as a therapeutic arsenal to target DNA binding proteins for effective treatment of diseases such as cancer.
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Affiliation(s)
- Jingwei Shao
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Arkansas for Medical SciencesLittle RockAR72205USA
| | - Yuqian Yan
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
| | - Donglin Ding
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
| | - Dejie Wang
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
| | - Yundong He
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
| | - Yunqian Pan
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
| | - Wei Yan
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Arkansas for Medical SciencesLittle RockAR72205USA
| | - Anupreet Kharbanda
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Arkansas for Medical SciencesLittle RockAR72205USA
| | - Hong‐yu Li
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Arkansas for Medical SciencesLittle RockAR72205USA
| | - Haojie Huang
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
- Department of UrologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
- Mayo Clinic Cancer CenterMayo Clinic College of Medicine and ScienceRochesterMN55905USA
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27
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Shin S, Zhou H, He C, Wei Y, Wang Y, Shingu T, Zeng A, Wang S, Zhou X, Li H, Zhang Q, Mo Q, Long J, Lan F, Chen Y, Hu J. Qki activates Srebp2-mediated cholesterol biosynthesis for maintenance of eye lens transparency. Nat Commun 2021; 12:3005. [PMID: 34021134 PMCID: PMC8139980 DOI: 10.1038/s41467-021-22782-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 03/23/2021] [Indexed: 02/04/2023] Open
Abstract
Defective cholesterol biosynthesis in eye lens cells is often associated with cataracts; however, how genes involved in cholesterol biosynthesis are regulated in lens cells remains unclear. Here, we show that Quaking (Qki) is required for the transcriptional activation of genes involved in cholesterol biosynthesis in the eye lens. At the transcriptome level, lens-specific Qki-deficient mice present downregulation of genes associated with the cholesterol biosynthesis pathway, resulting in a significant reduction of total cholesterol level in the eye lens. Mice with Qki depletion in lens epithelium display progressive accumulation of protein aggregates, eventually leading to cataracts. Notably, these defects are attenuated by topical sterol administration. Mechanistically, we demonstrate that Qki enhances cholesterol biosynthesis by recruiting Srebp2 and Pol II in the promoter regions of cholesterol biosynthesis genes. Supporting its function as a transcription co-activator, we show that Qki directly interacts with single-stranded DNA. In conclusion, we propose that Qki-Srebp2-mediated cholesterol biosynthesis is essential for maintaining the cholesterol level that protects lens from cataract development.
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Affiliation(s)
- Seula Shin
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Cancer Biology Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Hao Zhou
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenxi He
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yunfei Wang
- Clinical Science Division, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Takashi Shingu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ailiang Zeng
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaobo Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xin Zhou
- Cancer Research Institute of Jilin University, The First Hospital of Jilin University, Jilin, China
| | - Hongtao Li
- Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Qiang Zhang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qinling Mo
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin, China
| | - Jiafu Long
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin, China
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Hu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Cancer Biology Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
- Neuroscience Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
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28
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Lin M, Malik FK, Guo JT. A comparative study of protein-ssDNA interactions. NAR Genom Bioinform 2021; 3:lqab006. [PMID: 33655206 PMCID: PMC7902235 DOI: 10.1093/nargab/lqab006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/24/2020] [Accepted: 01/26/2021] [Indexed: 12/18/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play crucial roles in DNA replication, recombination and repair, and serve as key players in the maintenance of genomic stability. While a number of SSBs bind single-stranded DNA (ssDNA) non-specifically, the others recognize and bind specific ssDNA sequences. The mechanisms underlying this binding discrepancy, however, are largely unknown. Here, we present a comparative study of protein-ssDNA interactions by annotating specific and non-specific SSBs and comparing structural features such as DNA-binding propensities and secondary structure types of residues in SSB-ssDNA interactions, protein-ssDNA hydrogen bonding and π-π interactions between specific and non-specific SSBs. Our results suggest that protein side chain-DNA base hydrogen bonds are the major contributors to protein-ssDNA binding specificity, while π-π interactions may mainly contribute to binding affinity. We also found the enrichment of aspartate in the specific SSBs, a key feature in specific protein-double-stranded DNA (dsDNA) interactions as reported in our previous study. In addition, no significant differences between specific and non-specific groups with respect of conformational changes upon ssDNA binding were found, suggesting that the flexibility of SSBs plays a lesser role than that of dsDNA-binding proteins in conferring binding specificity.
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Affiliation(s)
- Maoxuan Lin
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Fareeha K Malik
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Research Center of Modeling and Simulation, National University of Science and Technology, Islamabad, 44000, Pakistan
| | - Jun-tao Guo
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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29
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Wang MC, McCown PJ, Schiefelbein GE, Brown JA. Secondary Structural Model of MALAT1 Becomes Unstructured in Chronic Myeloid Leukemia and Undergoes Structural Rearrangement in Cervical Cancer. Noncoding RNA 2021; 7:6. [PMID: 33450947 PMCID: PMC7838788 DOI: 10.3390/ncrna7010006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) influence cellular function through binding events that often depend on the lncRNA secondary structure. One such lncRNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), is upregulated in many cancer types and has a myriad of protein- and miRNA-binding sites. Recently, a secondary structural model of MALAT1 in noncancerous cells was proposed to form 194 hairpins and 13 pseudoknots. That study postulated that, in cancer cells, the MALAT1 structure likely varies, thereby influencing cancer progression. This work analyzes how that structural model is expected to change in K562 cells, which originated from a patient with chronic myeloid leukemia (CML), and in HeLa cells, which originated from a patient with cervical cancer. Dimethyl sulfate-sequencing (DMS-Seq) data from K562 cells and psoralen analysis of RNA interactions and structure (PARIS) data from HeLa cells were compared to the working structural model of MALAT1 in noncancerous cells to identify sites that likely undergo structural alterations. MALAT1 in K562 cells is predicted to become more unstructured, with almost 60% of examined hairpins in noncancerous cells losing at least half of their base pairings. Conversely, MALAT1 in HeLa cells is predicted to largely maintain its structure, undergoing 18 novel structural rearrangements. Moreover, 50 validated miRNA-binding sites are affected by putative secondary structural changes in both cancer types, such as miR-217 in K562 cells and miR-20a in HeLa cells. Structural changes unique to K562 cells and HeLa cells provide new mechanistic leads into how the structure of MALAT1 may mediate cancer in a cell-type specific manner.
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Affiliation(s)
| | | | | | - Jessica A. Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (M.C.W.); (P.J.M.); (G.E.S.)
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30
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Ghribi M, Nouemssi SB, Meddeb-Mouelhi F, Desgagné-Penix I. Genome Editing by CRISPR-Cas: A Game Change in the Genetic Manipulation of Chlamydomonas. Life (Basel) 2020; 10:E295. [PMID: 33233548 PMCID: PMC7699682 DOI: 10.3390/life10110295] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
Microalgae are promising photosynthetic unicellular eukaryotes among the most abundant on the planet and are considered as alternative sustainable resources for various industrial applications. Chlamydomonas is an emerging model for microalgae to be manipulated by multiple biotechnological tools in order to produce high-value bioproducts such as biofuels, bioactive peptides, pigments, nutraceuticals, and medicines. Specifically, Chlamydomonas reinhardtii has become a subject of different genetic-editing techniques adapted to modulate the production of microalgal metabolites. The main nuclear genome-editing tools available today include zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and more recently discovered the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein (Cas) nuclease system. The latter, shown to have an interesting editing capacity, has become an essential tool for genome editing. In this review, we highlight the available literature on the methods and the applications of CRISPR-Cas for C. reinhardtii genetic engineering, including recent transformation methods, most used bioinformatic tools, best strategies for the expression of Cas protein and sgRNA, the CRISPR-Cas mediated gene knock-in/knock-out strategies, and finally the literature related to CRISPR expression and modification approaches.
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Affiliation(s)
- Manel Ghribi
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada; (M.G.); (S.B.N.); (F.M.-M.)
| | - Serge Basile Nouemssi
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada; (M.G.); (S.B.N.); (F.M.-M.)
| | - Fatma Meddeb-Mouelhi
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada; (M.G.); (S.B.N.); (F.M.-M.)
- Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada; (M.G.); (S.B.N.); (F.M.-M.)
- Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
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31
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Mondal A, Bhattacherjee A. Mechanism of Dynamic Binding of Replication Protein A to ssDNA. J Chem Inf Model 2020; 60:5057-5069. [PMID: 32990435 DOI: 10.1021/acs.jcim.0c00564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Replication protein A (RPA) serves as a hub protein inside eukaryotic cells, where it coordinates crucial DNA metabolic processes and activates the DNA-damage response system. A characteristic feature of its action is to associate with single-stranded DNA (ssDNA) intermediates before handing them over to downstream proteins. The length of ssDNA intermediates differs for different pathways. This means that RPA must have mechanisms for selective processing of ssDNA intermediates based on their length, the knowledge of which is fundamental to elucidate when and how DNA repair and replication processes are symphonized. By employing extensive molecular dynamics simulations, we investigated the mechanism of binding of RPA to ssDNA of different lengths. We show that the binding involves dynamic equilibrium with a stable intermediate, the population of which increases with the length of ssDNA. The vital underlying factors are decoded through collective variable principal component analysis. It suggests a differently orchestrated set of interactions that define the action of RPA based on the length of ssDNA intermediates. We further estimated the association kinetics that matches excellently well with previous experimental studies and probed the diffusion mechanism of RPA to ssDNA. RPA diffuses on short ssDNA through progressive "bulge" formation. With long ssDNA, we observed a conformational change in ssDNA coupled with its binding to RPA in a cooperative fashion. This unanticipated binding mechanism successfully explains how the "short-lived", long ssDNA intermediates are processed quickly in vivo. This study thus reveals the molecular basis of several recent experimental observations related to RPA binding to ssDNA and provides novel insights into the RPA functioning in DNA repair and replication.
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Affiliation(s)
- Anupam Mondal
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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32
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Amarasekara CA, Athapattu US, Rathnayaka C, Choi J, Park S, Soper SA. Open-tubular nanoelectrochromatography (OT-NEC): gel-free separation of single stranded DNAs (ssDNAs) in thermoplastic nanochannels. Electrophoresis 2020; 41:1627-1640. [PMID: 33460211 DOI: 10.1002/elps.202000109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022]
Abstract
Electrophoresis or electrochromatography carried out in nanometer columns (width and depth) offers some attractive benefits compared to microscale columns. These advantages include unique separation mechanisms that are scale dependent, fast separation times, and simpler workflow due to the lack of a need for column packing and/or wall coatings to create a stationary phase. We report the use of thermoplastics, in this case PMMA, as the substrate for separating single-stranded DNAs (ssDNAs). Electrophoresis nanochannels were created in PMMA using nanoimprint lithography (NIL), which can produce devices at lower cost and in a higher production mode compared to the fabrication techniques required for glass devices. The nanochannel column in PMMA was successful in separating ssDNAs in free solution that was not possible using microchip electrophoresis in PMMA. The separation could be performed in <1 s with resolution >1.5 when carried out using at an electric field strength of 280 V/cm and an effective column length of 60 μm (100 nm × 100 nm, depth and width). The ssDNAs transport through the PMMA column was driven electrokinetically under the influence of an EOF. The results indicated that the separation was dominated by chromatographic effects using an open tubular nano-electrochromatography (OT-NEC) mode of separation. Interesting to these separations was that no column packing was required nor a wall coating to create the stationary phase; the separation was affected using the native polymer that was UV/O3 activated and an aqueous buffer mobile phase.
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Affiliation(s)
- Charuni A Amarasekara
- Department of Chemistry, The University of Kansas, Lawrence, Kansas, USA.,Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA
| | - Uditha S Athapattu
- Department of Chemistry, The University of Kansas, Lawrence, Kansas, USA.,Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA
| | - Chathurika Rathnayaka
- Department of Chemistry, The University of Kansas, Lawrence, Kansas, USA.,Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA
| | - Junseo Choi
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA.,Department of Mechanical Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Sunggook Park
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA.,Department of Mechanical Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Steven A Soper
- Department of Chemistry, The University of Kansas, Lawrence, Kansas, USA.,Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas, USA.,Department of Mechanical Engineering, Louisiana State University, Baton Rouge, Louisiana, USA.,Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas, USA.,Bioengineering Program, The University of Kansas, Lawrence, Kansas, USA.,KU Cancer Center, University of Kansas Medical Center, Kansas City, Kansas, USA
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33
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Cohen IR, Marron A. The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction. F1000Res 2020; 9:626. [PMID: 32802320 PMCID: PMC7416572 DOI: 10.12688/f1000research.24447.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/11/2020] [Indexed: 11/13/2023] Open
Abstract
The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not. Interactions, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosters survival-of-the-fitted - those entities that resist entropic destruction - and not only of the fittest - the entities with the greatest reproductive success. The "unit" of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are "fit enough". We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.
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Affiliation(s)
- Irun R. Cohen
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Assaf Marron
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
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34
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Cohen IR, Marron A. The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction. F1000Res 2020; 9:626. [PMID: 32802320 PMCID: PMC7416572 DOI: 10.12688/f1000research.24447.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/26/2020] [Indexed: 11/20/2022] Open
Abstract
The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not. Interactions, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosters survival-of-the-fitted - those entities that resist entropic destruction - and not only of the fittest - the entities with the greatest reproductive success. The "unit" of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are "fit enough". We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.
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Affiliation(s)
- Irun R. Cohen
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Assaf Marron
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
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35
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Cohen IR, Marron A. The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction. F1000Res 2020; 9:626. [PMID: 32802320 PMCID: PMC7416572 DOI: 10.12688/f1000research.24447.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/22/2020] [Indexed: 11/13/2023] Open
Abstract
The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not. Interactions, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosters survival-of-the-fitted - those entities that resist entropic destruction - and not only of the fittest - the entities with the greatest reproductive success. The "unit" of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are "fit enough". We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.
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Affiliation(s)
- Irun R. Cohen
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Assaf Marron
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
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Park HJ, Ko HL, Won DH, Hwang DB, Shin YS, Kwak HW, Kim HJ, Yun JW, Nam JH. Comprehensive Analysis of the Safety Profile of a Single-Stranded RNA Nano-Structure Adjuvant. Pharmaceutics 2019; 11:pharmaceutics11090464. [PMID: 31500241 PMCID: PMC6781302 DOI: 10.3390/pharmaceutics11090464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 01/01/2023] Open
Abstract
Adjuvants enhance the efficacy of vaccines by stimulating immune response-related gene expression and pathways. Although some adjuvants have been approved for commercial use in human vaccines (e.g., Alum, MF59, and AS03), they might elicit adverse side effects, such as autoimmune diseases. Recently, we developed a novel single-stranded RNA (ssRNA) nano-structure adjuvant, which can stimulate both Th1 and Th2 responses. In this study, we evaluated the safety and toxicological profiles of this ssRNA nano-structure adjuvant in vitro and in vivo. Mice were intramuscularly immunized with the ssRNA nano-structure adjuvant three times, once every 2 weeks. The results indicate no significant differences in hematological and serum biochemistry parameters between the ssRNA-treated groups and the control group. From a histopathological perspective, no evidence of tissue damage was found in any group. The levels of IgE and anti-nuclear antibodies, which are markers of autoimmune disease, were not different between the ssRNA-treated groups and the control group. The findings of this study suggest that the ssRNA nano-structure can be used as a safe adjuvant to increase vaccine efficacies.
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Affiliation(s)
- Hyeong-Jun Park
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Korea.
| | - Hae Li Ko
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Korea.
| | - Dong-Hoon Won
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Korea.
| | - Da-Bin Hwang
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Korea.
| | - Yoo-Sub Shin
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Korea.
| | - Hye-Won Kwak
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Korea.
| | - Hye-Jung Kim
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Korea.
| | - Jun-Won Yun
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Korea.
| | - Jae-Hwan Nam
- Department of Biotechnology, The Catholic University of Korea, Bucheon 14662, Korea.
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