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Colbert BM, Lanting C, Smeal M, Blanton S, Dykxhoorn DM, Tang PC, Getchell RL, Velde H, Fehrmann M, Thorpe R, Chapagain P, Elkhaligy H, Kremer H, Yntema H, Haer-Wigman L, Redfield S, Sun T, Bruijn S, Plomp A, Goderie T, van de Kamp J, Free RH, Wassink-Ruiter JK, Widdershoven J, Vanhoutte E, Rotteveel L, Kriek M, van Dooren M, Hoefsloot L, de Gier HHW, Schaefer A, Kolbe D, Azaiez H, Rabie G, Aburayyan A, Kawas M, Kanaan M, Holder J, Usami SI, Chen Z, Dai P, Holt J, Nelson R, Choi BY, Shearer E, Smith RJH, Pennings R, Liu XZ. The natural history and genotype-phenotype correlations of TMPRSS3 hearing loss: an international, multi-center, cohort analysis. Hum Genet 2024:10.1007/s00439-024-02648-3. [PMID: 38691166 DOI: 10.1007/s00439-024-02648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/21/2024] [Indexed: 05/03/2024]
Abstract
TMPRSS3-related hearing loss presents challenges in correlating genotypic variants with clinical phenotypes due to the small sample sizes of previous studies. We conducted a cross-sectional genomics study coupled with retrospective clinical phenotype analysis on 127 individuals. These individuals were from 16 academic medical centers across 6 countries. Key findings revealed 47 unique TMPRSS3 variants with significant differences in hearing thresholds between those with missense variants versus those with loss-of-function genotypes. The hearing loss progression rate for the DFNB8 subtype was 0.3 dB/year. Post-cochlear implantation, an average word recognition score of 76% was observed. Of the 51 individuals with two missense variants, 10 had DFNB10 with profound hearing loss. These 10 all had at least one of 4 TMPRSS3 variants predicted by computational modeling to be damaging to TMPRSS3 structure and function. To our knowledge, this is the largest study of TMPRSS3 genotype-phenotype correlations. We find significant differences in hearing thresholds, hearing loss progression, and age of presentation, by TMPRSS3 genotype and protein domain affected. Most individuals with TMPRSS3 variants perform well on speech recognition tests after cochlear implant, however increased age at implant is associated with worse outcomes. These findings provide insight for genetic counseling and the on-going design of novel therapeutic approaches.
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Affiliation(s)
- Brett M Colbert
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL, 33136, USA
- Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, USA
| | - Cris Lanting
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Molly Smeal
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL, 33136, USA
| | - Susan Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL, 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, USA
| | - Derek M Dykxhoorn
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, USA
| | - Pei-Ciao Tang
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL, 33136, USA
| | - Richard L Getchell
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, USA
| | - Hedwig Velde
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mirthe Fehrmann
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ryan Thorpe
- Department of Otolaryngology, University of Iowa, Iowa City, USA
| | - Prem Chapagain
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, USA
| | - Heidy Elkhaligy
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, USA
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger Yntema
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Tieqi Sun
- Boston Children's Hospital, Boston, USA
| | - Saskia Bruijn
- Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Astrid Plomp
- Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Thadé Goderie
- Amsterdam University Medical Center, Amsterdam, The Netherlands
| | | | - Rolien H Free
- Groningen University Medical Center, Groningen, The Netherlands
| | | | | | - Els Vanhoutte
- Maastricht University Medical Center, Maastricht, The Netherlands
| | | | | | | | | | | | - Amanda Schaefer
- Department of Otolaryngology, University of Iowa, Iowa City, USA
| | - Diana Kolbe
- Department of Otolaryngology, University of Iowa, Iowa City, USA
| | - Hela Azaiez
- Department of Otolaryngology, University of Iowa, Iowa City, USA
| | - Grace Rabie
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, Palestine
| | | | - Mariana Kawas
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, Palestine
| | - Moien Kanaan
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, Palestine
| | | | | | - Zhengyi Chen
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary and Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, USA
| | - Pu Dai
- PLA General Hospital, Beijing, China
| | | | - Rick Nelson
- Department of Otolaryngology, Indiana University School of Medicine, Indianapolis, USA
| | - Byung Yoon Choi
- Seoul National University Bundang Hospital, Seongnam, South Korea
| | | | | | - Ronald Pennings
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, 1120 NW 14th Street, 5th Floor, Miami, FL, 33136, USA.
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, USA.
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Gressett TE, Hossen ML, Talkington G, Volic M, Perez H, Tiwari PB, Chapagain P, Bix G. Molecular interactions between perlecan LG3 and the SARS-CoV-2 spike protein receptor binding domain. Protein Sci 2024; 33:e4843. [PMID: 37996967 PMCID: PMC10731540 DOI: 10.1002/pro.4843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/14/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a global health crisis with significant clinical morbidity and mortality. While angiotensin-converting enzyme 2 (ACE2) is the primary receptor for viral entry, other cell surface and extracellular matrix proteins may also bind to the viral receptor binding domain (RBD) within the SARS-CoV-2 spike protein. Recent studies have implicated heparan sulfate proteoglycans, specifically perlecan LG3, in facilitating SARS-CoV-2 binding to ACE2. However, the role of perlecan LG3 in SARS-CoV-2 pathophysiology is not well understood. In this study, we investigated the binding interactions between the SARS-CoV-2 spike protein RBD and perlecan LG3 through molecular modeling simulations and surface plasmon resonance (SPR) experiments. Our results indicate stable binding between LG3 and SARS-CoV-2 spike protein RBD, which may potentially enhance RBD-ACE2 interactions. These findings shed light on the role of perlecan LG3 in SARS-CoV-2 infection and provide insight into SARS-CoV-2 pathophysiology and potential therapeutic strategy for COVID-19.
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Affiliation(s)
- Timothy E. Gressett
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
| | - Md Lokman Hossen
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Department of PhysicsUniversity of BarishalKornokathiBangladesh
| | - Grant Talkington
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
| | - Milla Volic
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
| | - Hugo Perez
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
| | | | - Prem Chapagain
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Biomolecular Sciences InstituteFlorida International UniversityMiamiFloridaUSA
| | - Gregory Bix
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
- Department of NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
- Department of Microbiology and ImmunologyTulane University School of MedicineNew OrleansLouisianaUSA
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3
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Yuan M, Mahmud I, Katsushima K, Joshi K, Saulnier O, Pokhrel R, Lee B, Liyanage W, Kunhiraman H, Stapleton S, Gonzalez-Gomez I, Kannan RM, Eisemann T, Kolanthai E, Seal S, Garrett TJ, Abbasi S, Bockley K, Hanes J, Chapagain P, Jallo G, Wechsler-Reya RJ, Taylor MD, Eberhart CG, Ray A, Perera RJ. miRNA-211 maintains metabolic homeostasis in medulloblastoma through its target gene long-chain acyl-CoA synthetase 4. Acta Neuropathol Commun 2023; 11:203. [PMID: 38115140 PMCID: PMC10729563 DOI: 10.1186/s40478-023-01684-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 11/05/2023] [Indexed: 12/21/2023] Open
Abstract
The prognosis of childhood medulloblastoma (MB) is often poor, and it usually requires aggressive therapy that adversely affects quality of life. microRNA-211 (miR-211) was previously identified as an important regulator of cells that descend from neural cells. Since medulloblastomas primarily affect cells with similar ontogeny, we investigated the role and mechanism of miR-211 in MB. Here we showed that miR-211 expression was highly downregulated in cell lines, PDXs, and clinical samples of different MB subgroups (SHH, Group 3, and Group 4) compared to normal cerebellum. miR-211 gene was ectopically expressed in transgenic cells from MB subgroups, and they were subjected to molecular and phenotypic investigations. Monoclonal cells stably expressing miR-211 were injected into the mouse cerebellum. miR-211 forced expression acts as a tumor suppressor in MB both in vitro and in vivo, attenuating growth, promoting apoptosis, and inhibiting invasion. In support of emerging regulatory roles of metabolism in various forms of cancer, we identified the acyl-CoA synthetase long-chain family member (ACSL4) as a direct miR-211 target. Furthermore, lipid nanoparticle-coated, dendrimer-coated, and cerium oxide-coated miR-211 nanoparticles were applied to deliver synthetic miR-211 into MB cell lines and cellular responses were assayed. Synthesizing nanoparticle-miR-211 conjugates can suppress MB cell viability and invasion in vitro. Our findings reveal miR-211 as a tumor suppressor and a potential therapeutic agent in MB. This proof-of-concept paves the way for further pre-clinical and clinical development.
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Affiliation(s)
- Menglang Yuan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Iqbal Mahmud
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Keisuke Katsushima
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Kandarp Joshi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Olivier Saulnier
- The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rudramani Pokhrel
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Bongyong Lee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Wathsala Liyanage
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Haritha Kunhiraman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Stacie Stapleton
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Ignacio Gonzalez-Gomez
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Rangaramanujam M Kannan
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Tanja Eisemann
- National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Elayaraja Kolanthai
- Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center, Materials Science and Engineering, College of Medicine, University of Central Florida, Orlando, FL, 32826, USA
| | - Sudipta Seal
- Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center, Materials Science and Engineering, College of Medicine, University of Central Florida, Orlando, FL, 32826, USA
| | - Timothy J Garrett
- Department Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Saed Abbasi
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Kimberly Bockley
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Justin Hanes
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL, 33199, USA
| | - George Jallo
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Robert J Wechsler-Reya
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Texas Children's Cancer Center, Hematology-Oncology Section, Houston, TX, 77030, USA
- Department of Pediatrics-Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Charles G Eberhart
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Animesh Ray
- Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Ranjan J Perera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA.
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA.
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4
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Deng Z, Chapagain P, Leng F. Macromolecular crowding potently stimulates DNA supercoiling activity of Mycobacterium tuberculosis DNA gyrase. J Biol Chem 2023; 299:105439. [PMID: 37944619 PMCID: PMC10731242 DOI: 10.1016/j.jbc.2023.105439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Macromolecular crowding, manifested by high concentrations of proteins and nucleic acids in living cells, significantly influences biological processes such as enzymatic reactions. Studying these reactions in vitro, using agents such as polyetthylene glycols (PEGs) and polyvinyl alcohols (PVAs) to mimic intracellular crowding conditions, is essential due to the notable differences from enzyme behaviors observed in diluted aqueous solutions. In this article, we studied Mycobacterium tuberculosis (Mtb) DNA gyrase under macromolecular crowding conditions by incorporating PEGs and PVAs into the DNA supercoiling reactions. We discovered that high concentrations of potassium glutamate, glycine betaine, PEGs, and PVA substantially stimulated the DNA supercoiling activity of Mtb DNA gyrase. Steady-state kinetic studies showed that glycine betaine and PEG400 significantly reduced the KM of Mtb DNA gyrase and simultaneously increased the Vmax or kcat of Mtb DNA gyrase for ATP and the plasmid DNA molecule. Molecular dynamics simulation studies demonstrated that PEG molecules kept the ATP lid of DNA gyrase subunit B in a closed or semiclosed conformation, which prevented ATP molecules from leaving the ATP-binding pocket of DNA gyrase subunit B. The stimulation of the DNA supercoiling activity of Mtb DNA gyrase by these molecular crowding agents likely results from a decrease in water activity and an increase in excluded volume.
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Affiliation(s)
- Zifang Deng
- Biomolecular Science Institute, Florida International University, Miami, Florida, USA; Department of Chemistry & Biochemistry, Florida International University, Miami, Florida, USA
| | - Prem Chapagain
- Biomolecular Science Institute, Florida International University, Miami, Florida, USA; Department of Physics, Florida International University, Miami, Florida, USA
| | - Fenfei Leng
- Biomolecular Science Institute, Florida International University, Miami, Florida, USA; Department of Chemistry & Biochemistry, Florida International University, Miami, Florida, USA.
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5
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Magaña AJ, Sklenicka J, Pinilla C, Giulianotti M, Chapagain P, Santos R, Ramirez MS, Tolmasky ME. Restoring susceptibility to aminoglycosides: identifying small molecule inhibitors of enzymatic inactivation. RSC Med Chem 2023; 14:1591-1602. [PMID: 37731693 PMCID: PMC10507813 DOI: 10.1039/d3md00226h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Growing resistance to antimicrobial medicines is a critical health problem that must be urgently addressed. Adding to the increasing number of patients that succumb to infections, there are other consequences to the rise in resistance like the compromise of several medical procedures and dental work that are heavily dependent on infection prevention. Since their introduction in the clinics, aminoglycoside antibiotics have been a critical component of the armamentarium to treat infections. Still, the increase in resistance and their side effects led to a decline in their utilization. However, numerous current factors, like the urgent need for antimicrobials and their favorable properties, led to renewed interest in these drugs. While efforts to design new classes of aminoglycosides refractory to resistance mechanisms and with fewer toxic effects are starting to yield new promising molecules, extending the useful life of those already in use is essential. For this, numerous research projects are underway to counter resistance from different angles, like inhibition of expression or activity of resistance components. This review focuses on selected examples of one aspect of this quest, the design or identification of small molecule inhibitors of resistance caused by enzymatic modification of the aminoglycoside. These compounds could be developed as aminoglycoside adjuvants to overcome resistant infections.
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Affiliation(s)
- Angel J Magaña
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Jan Sklenicka
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Clemencia Pinilla
- Center for Translational Science, Florida International University Port St. Lucie FL 34987 USA
| | - Marc Giulianotti
- Center for Translational Science, Florida International University Port St. Lucie FL 34987 USA
| | - Prem Chapagain
- Department of Physics, Florida International University Miami FL 33199 USA
- Biomolecular Sciences Institute, Florida International University Miami FL 33199 USA
| | - Radleigh Santos
- Department of Mathematics, Nova Southeastern University Fort Lauderdale FL 33314 USA
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton Fullerton CA 92831 USA
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Sharma T, Gerstman B, Chapagain P. Distinctive Features of the XBB.1.5 and XBB.1.16 Spike Protein Receptor-Binding Domains and Their Roles in Conformational Changes and Angiotensin-Converting Enzyme 2 Binding. Int J Mol Sci 2023; 24:12586. [PMID: 37628766 PMCID: PMC10454900 DOI: 10.3390/ijms241612586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The emergence and the high transmissibility of the XBB.1.5 and XBB.1.16 subvariants of the SARS-CoV-2 omicron has reignited concerns over the potential impact on vaccine efficacy for these and future variants. We investigated the roles of the XBB.1.5 and XBB.1.16 mutations on the structure of the spike protein's receptor-binding domain (RBD) and its interactions with the host cell receptor ACE2. To bind to ACE2, the RBD must transition from the closed-form to the open-form configuration. We found that the XBB variants have less stable closed-form structures that may make the transition to the open-form easier. We found that the mutations enhance the RBD-ACE2 interactions in XBB.1.16 compared to XBB.1.5. We observed significant structural changes in the loop and motif regions of the RBD, altering well-known antibody-binding sites and potentially rendering primary RBD-specific antibodies ineffective. Our findings elucidate how subtle structural changes and interactions contribute to the subvariants' fitness over their predecessors.
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Affiliation(s)
- Tej Sharma
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Bernard Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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7
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Yuan Y, Yan D, Skidmore J, Chapagain P, Liu X, He S. Responsiveness of the electrically stimulated cochlear nerve in patients with a missense variant in ACTG1: Preliminary Results. Front Audiol Otol 2023; 1:1213323. [PMID: 38590973 PMCID: PMC11000624 DOI: 10.3389/fauot.2023.1213323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
This preliminary study identified a missense variant in ACTG1 (NM_001614.5) in a family with autosomal dominant non-syndromic hearing loss (ADNSHL). The responsiveness of the electrically-stimulated cochlear nerve (CN) in two implanted participants with this missense change was also evaluated and reported. Genetic testing was done using a custom capture panel (MiamiOtoGenes) and whole exome sequencing. The responsiveness of the electrically-stimulated CN was evaluated in two members of this family (G1 and G4) using the electrically evoked compound action potential (eCAP). eCAP results from these two participants were compared with those measured three implanted patient populations: children with cochlear nerve deficiency, children with idiopathic hearing loss and normal-sized cochlear nerves, and postligually deafened adults. Sequencing of ACTG1 identified a missense c.737A>T (p. Gln246Leu) variant in ACTG1 (NM_001614.5) which is most likely the genetic cause of ADNSHL in this family. eCAP results measured in these two participants showed substantial variations. The results indicated the missense c.737A>T (p. Gln246Leu) variant in ACTG1 (NM_001614.5) co-segregated with hearing loss in this family. The responsiveness of the electrically-stimulated CN can vary among patients with the same genetic variants, which suggests the importance of evaluating the functional status of the CN for individual CI patients.
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Affiliation(s)
- Yi Yuan
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Denise Yan
- Department of Otolaryngology – Head & Neck Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jeffrey Skidmore
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Prem Chapagain
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Xuezhong Liu
- Department of Otolaryngology – Head & Neck Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T. MacDonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Shuman He
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Department of Audiology, Nationwide Children’s Hospital, Columbus, Ohio, USA
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8
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Vashist A, Raymond AD, Chapagain P, Vashist A, Arias AY, Kolishetti N, Nair M. Multi-functional auto-fluorescent nanogels for theranostics. J Neurovirol 2023; 29:252-257. [PMID: 37248372 PMCID: PMC10404193 DOI: 10.1007/s13365-023-01138-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 05/31/2023]
Abstract
Here in the present article, the state of art for nanotechnology-enabled nanogel theranostics and the upcoming concepts in nanogel-based therapeutics are summarized. The benefits, innovation, and prospects of nanogel technology are also briefly presented.
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Affiliation(s)
- Arti Vashist
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
- Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
| | - Andrea D. Raymond
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
- Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
| | - Prem Chapagain
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, FL 33199 USA
| | - Atul Vashist
- Department of Infection & Immunology, Translational Health Science and Technology, Faridabad, Haryana 121001 India
| | - Adriana Yndart Arias
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
- Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
| | - Nagesh Kolishetti
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
- Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
| | - Madhavan Nair
- Department of Immunology and Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
- Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
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9
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Katsushima K, Pokhrel R, Mahmud I, Yuan M, Murad R, Baral P, Zhou R, Chapagain P, Garrett T, Stapleton S, Jallo G, Bettegowda C, Raabe E, Wechsler-Reya RJ, Eberhart CG, Perera RJ. The oncogenic circular RNA circ_63706 is a potential therapeutic target in sonic hedgehog-subtype childhood medulloblastomas. Acta Neuropathol Commun 2023; 11:38. [PMID: 36899402 PMCID: PMC10007801 DOI: 10.1186/s40478-023-01521-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 03/12/2023] Open
Abstract
Medulloblastoma (MB) develops through various genetic, epigenetic, and non-coding (nc) RNA-related mechanisms, but the roles played by ncRNAs, particularly circular RNAs (circRNAs), remain poorly defined. CircRNAs are increasingly recognized as stable non-coding RNA therapeutic targets in many cancers, but little is known about their function in MBs. To determine medulloblastoma subgroup-specific circRNAs, publicly available RNA sequencing (RNA-seq) data from 175 MB patients were interrogated to identify circRNAs that differentiate between MB subgroups. circ_63706 was identified as sonic hedgehog (SHH) group-specific, with its expression confirmed by RNA-FISH analysis in clinical tissue samples. The oncogenic function of circ_63706 was characterized in vitro and in vivo. Further, circ_63706-depleted cells were subjected to RNA-seq and lipid profiling to identify its molecular function. Finally, we mapped the circ_63706 secondary structure using an advanced random forest classification model and modeled a 3D structure to identify its interacting miRNA partner molecules. Circ_63706 regulates independently of the host coding gene pericentrin (PCNT), and its expression is specific to the SHH subgroup. circ_63706-deleted cells implanted into mice produced smaller tumors, and mice lived longer than parental cell implants. At the molecular level, circ_63706-deleted cells elevated total ceramide and oxidized lipids and reduced total triglyceride. Our study implicates a novel oncogenic circular RNA in the SHH medulloblastoma subgroup and establishes its molecular function and potential as a future therapeutic target.
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Affiliation(s)
- Keisuke Katsushima
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA.,Johns Hopkins All Children's Hospital, St. Petersburg, USA
| | - Rudramani Pokhrel
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA.,Johns Hopkins All Children's Hospital, St. Petersburg, USA
| | - Iqbal Mahmud
- Department Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, USA.,Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Menglang Yuan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA.,Johns Hopkins All Children's Hospital, St. Petersburg, USA
| | - Rabi Murad
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, USA
| | - Prabin Baral
- Department of Physics, Florida International University, Miami, USA
| | - Rui Zhou
- Johns Hopkins All Children's Hospital, St. Petersburg, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, USA.,Biomolecular Sciences Institute, Florida International University, Miami, USA
| | - Timothy Garrett
- Department Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, USA
| | | | - George Jallo
- Johns Hopkins All Children's Hospital, St. Petersburg, USA.,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Chetan Bettegowda
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA.,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Eric Raabe
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA
| | | | - Charles G Eberhart
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Ranjan J Perera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA. .,Johns Hopkins All Children's Hospital, St. Petersburg, USA. .,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, USA.
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10
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Tsegay PS, Hernandez D, Qu F, Olatunji M, Mamun Y, Chapagain P, Liu Y. RNA-guided DNA base damage repair via DNA polymerase-mediated nick translation. Nucleic Acids Res 2022; 51:166-181. [PMID: 36533524 PMCID: PMC9841414 DOI: 10.1093/nar/gkac1178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/28/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
DNA repair is mediated by DNA synthesis guided by a DNA template. Recent studies have shown that DNA repair can also be accomplished by RNA-guided DNA synthesis. However, it remains unknown how RNA can guide DNA synthesis to repair DNA damage. In this study, we revealed the molecular mechanisms underlying RNA-guided DNA synthesis and base damage repair mediated by human repair DNA polymerases. We showed that pol β, pol κ, and pol ι predominantly synthesized one nucleotide, and pol η, pol ν, and pol θ synthesized multi-nucleotides during RNA-guided DNA base damage repair. The steady-state kinetics showed that pol η exhibited more efficient RNA-guided DNA synthesis than pol β. Using molecular dynamics simulation, we further revealed dynamic conformational changes of pol β and pol η and their structural basis to accommodate the RNA template and misoriented triphosphates of an incoming nucleotide. We demonstrated that RNA-guided base damage repair could be accomplished by the RNA-guided DNA strand-displacement synthesis and nick translation leading to nick ligation in a double-strand DNA region. Our study revealed a novel RNA-guided base damage repair pathway during transcription and DNA replication.
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Affiliation(s)
- Pawlos S Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Daniela Hernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Fei Qu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Mustapha Olatunji
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Yasir Mamun
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL, USA,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Yuan Liu
- To whom correspondence should be addressed. Tel: +1 305 348 3628; Fax: +1 305 348 2772;
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11
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Alfonso EE, Troche R, Deng Z, Annamalai T, Chapagain P, Tse-Dinh YC, Leng F. Potent Inhibition of Bacterial DNA Gyrase by Digallic Acid and Other Gallate Derivatives. ChemMedChem 2022; 17:e202200301. [PMID: 36161274 PMCID: PMC9742164 DOI: 10.1002/cmdc.202200301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/23/2022] [Indexed: 01/14/2023]
Abstract
Bacterial DNA gyrase, an essential enzyme, is a validated target for discovering and developing new antibiotics. Here we screened a pool of polyphenols and discovered that digallic acid is a potent DNA gyrase inhibitor. We also found that several food additives based on gallate, such as dodecyl gallate, potently inhibit bacterial DNA gyrase. Interestingly, the IC50 of these gallate derivatives against DNA gyrase is correlated with the length of hydrocarbon chain connecting to the gallate. These new bacterial DNA gyrase inhibitors are ATP competitive inhibitors of DNA gyrase. Our results also show that digallic acid and certain gallate derivatives potently inhibit E. coli DNA topoisomerase IV. Several gallate derivatives have strong antimicrobial activities against Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA). This study provides a solid foundation for the design and synthesis of gallate-based DNA gyrase inhibitors that may be used to combat antibacterial resistance.
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Affiliation(s)
- Eddy E Alfonso
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Rogelio Troche
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Zifang Deng
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Thirunavukkarasu Annamalai
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Prem Chapagain
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
- Department of Physics, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yuk-Ching Tse-Dinh
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
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12
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Alfonso EE, Deng Z, Boaretto D, Hood BL, Vasile S, Smith LH, Chambers JW, Chapagain P, Leng F. Novel and Structurally Diversified Bacterial DNA Gyrase Inhibitors Discovered through a Fluorescence-Based High-Throughput Screening Assay. ACS Pharmacol Transl Sci 2022; 5:932-944. [PMID: 36268121 PMCID: PMC9578135 DOI: 10.1021/acsptsci.2c00113] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Indexed: 12/25/2022]
Abstract
Bacterial DNA gyrase, a type IIA DNA topoisomerase that plays an essential role in bacterial DNA replication and transcription, is a clinically validated target for discovering and developing new antibiotics. In this article, based on a supercoiling-dependent fluorescence quenching (SDFQ) method, we developed a high-throughput screening (HTS) assay to identify inhibitors targeting bacterial DNA gyrase and screened the National Institutes of Health's Molecular Libraries Small Molecule Repository library containing 370,620 compounds in which 2891 potential gyrase inhibitors have been identified. According to these screening results, we acquired 235 compounds to analyze their inhibition activities against bacterial DNA gyrase using gel- and SDFQ-based DNA gyrase inhibition assays and discovered 155 new bacterial DNA gyrase inhibitors with a wide structural diversity. Several of them have potent antibacterial activities. These newly discovered gyrase inhibitors include several DNA gyrase poisons that stabilize the gyrase-DNA cleavage complexes and provide new chemical scaffolds for the design and synthesis of bacterial DNA gyrase inhibitors that may be used to combat multidrug-resistant bacterial pathogens. Additionally, this HTS assay can be applied to screen inhibitors against other DNA topoisomerases.
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Affiliation(s)
- Eddy E. Alfonso
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United
States
| | - Zifang Deng
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United
States
| | - Daniel Boaretto
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United
States
| | - Becky L. Hood
- Conrad
Prebys Center for Chemical Genomics, Sanford
Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Stefan Vasile
- Conrad
Prebys Center for Chemical Genomics, Sanford
Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Layton H. Smith
- Conrad
Prebys Center for Chemical Genomics, Sanford
Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Jeremy W. Chambers
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Environmental Health Sciences, Florida
International University, Miami, Florida 33199, United States
| | - Prem Chapagain
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Physics, Florida International University, Miami, Florida 33199, United States
| | - Fenfei Leng
- Biomolecular
Sciences Institute, Florida International
University, Miami, Florida 33199, United States
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United
States
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13
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Pokhrel R, Shakya R, Baral P, Chapagain P. Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus. J Chem Inf Model 2022; 62:4955-4962. [PMID: 35981320 DOI: 10.1021/acs.jcim.2c00437] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The peptidoglycan (PG) layer is a vital component of the bacterial cell wall that protects the cell from rupturing due to internal pressure. Its ubiquity across the bacterial kingdom but not animals has made it the target of drug discovery efforts. The PG layer composed of cross-linked PG strands is porous enough to allow the diffusion of molecules through the PG mesh and into the cell. The lack of an accurate atomistic model of the PG mesh has limited the computational investigations of drug diffusion in Gram-positive bacteria, which lack the outer membrane but consist of a much thicker PG layer compared to Gram-negative bacteria. In this work, we built an atomistic model of the Staphylococcus aureus PG layer architecture with horizontally aligned PG strands and performed molecular dynamics simulations of the diffusion of curcumin molecules through the PG mesh. An accurate model of the Gram-positive bacterial cell wall may aid in developing novel antibiotics to tackle the threat posed by antibiotic resistance.
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Affiliation(s)
- Rudramani Pokhrel
- Department of Physics, Florida International University, Miami, Florida 33199, United States
| | - Rojesh Shakya
- Department of Physics, Florida International University, Miami, Florida 33199, United States
| | - Prabin Baral
- Department of Physics, Florida International University, Miami, Florida 33199, United States
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, Florida 33199, United States.,Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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14
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Barrios A, Milan M, Perozo E, Hossen ML, Chapagain P, Moon JH. Effects of sidechain isomerism on polymer-based non-covalent protein delivery. Chem Commun (Camb) 2022; 58:8246-8249. [PMID: 35786710 DOI: 10.1039/d2cc02343a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the importance of functional group isomerism on intracellular protein delivery using polymers containing different isomeric side chains. While the physical properties of polymer/protein complexes are relatively similar, different planarity of the isomers greatly influences the cellular entry efficiency.
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Affiliation(s)
- Alfonso Barrios
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA.
| | - Mario Milan
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA.
| | - Elianny Perozo
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA.
| | - Md Lokman Hossen
- Department of Physics, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA.,Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA
| | - Joong Ho Moon
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA. .,Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA
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15
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Devadoss D, Acharya A, Manevski M, Houserova D, Cioffi MD, Pandey K, Nair M, Chapagain P, Mirsaeidi M, Borchert GM, Byrareddy SN, Chand HS. Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype. iScience 2022; 25:104685. [PMID: 35789750 PMCID: PMC9242679 DOI: 10.1016/j.isci.2022.104685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/25/2022] [Accepted: 06/23/2022] [Indexed: 01/20/2023] Open
Abstract
Noncoding RNAs are important regulators of mucoinflammatory response, but little is known about the contribution of airway long noncoding RNAs (lncRNAs) in COVID-19. RNA-seq analysis showed a more than 4-fold increased expression of IL-6, ICAM-1, CXCL-8, and SCGB1A1 inflammatory factors; MUC5AC and MUC5B mucins; and SPDEF, FOXA3, and FOXJ1 transcription factors in COVID-19 patient nasal samples compared with uninfected controls. A lncRNA on antisense strand to ICAM-1 or LASI was induced 2-fold in COVID-19 patients, and its expression was directly correlated with viral loads. A SARS-CoV-2-infected 3D-airway model largely recapitulated these clinical findings. RNA microscopy and molecular modeling indicated a possible interaction between viral RNA and LASI lncRNA. Notably, blocking LASI lncRNA reduced the SARS-CoV-2 replication and suppressed MUC5AC mucin levels and associated inflammation, and select LASI-dependent miRNAs (e.g., let-7b-5p and miR-200a-5p) were implicated. Thus, LASI lncRNA represents an essential facilitator of SARS-CoV-2 infection and associated airway mucoinflammatory response.
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Affiliation(s)
- Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Dominika Houserova
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Michael D. Cioffi
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Madhavan Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA,Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Mehdi Mirsaeidi
- Miller School of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Miami, Miami, FL 33136, USA
| | - Glen M. Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA,Corresponding author
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA,Corresponding author
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16
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Hossen ML, Baral P, Sharma T, Gerstman BS, Chapagain P. Significance of the RBD mutations in the SARS-CoV-2 Omicron: from spike opening to antibody escape and cell attachment. Phys Chem Chem Phys 2022; 24:9123-9129. [DOI: 10.1039/d2cp00169a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We computationally investigated the role of the Omicron RBD mutations on its structure and interactions with surrounding domains in the spike trimer as well as with ACE2. Our results suggest...
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17
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Tsegay PS, Hernandez D, Brache C, Chatgilialoglu C, Krokidis MG, Chapagain P, Liu Y. Incorporation of 5',8-cyclo-2'deoxyadenosines by DNA repair polymerases via base excision repair. DNA Repair (Amst) 2022; 109:103258. [PMID: 34871863 PMCID: PMC9884144 DOI: 10.1016/j.dnarep.2021.103258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 10/30/2021] [Accepted: 11/18/2021] [Indexed: 01/31/2023]
Abstract
5',8-cyclo-2-deoxy nucleosides (cdPus) are the smallest tandem purine lesions including 5',8-cyclo-2'-deoxyadenosine (cdA) and 5',8-cyclo-2'-deoxyguanosine (cdG). They can inhibit DNA and RNA polymerases causing mutations, DNA strand breaks, and termination of DNA replication and gene transcription. cdPus can be removed by nucleotide excision repair with low efficiency allowing them to accumulate in the genome. Recent studies suggest that cdPus can be induced in damaged nucleotide pools and incorporated into the genome by DNA polymerases. However, it remains unknown if and how DNA polymerases can incorporate cdPus. In this study, we examined the incorporation of cdAs by human DNA repair polymerases, DNA polymerases β (pol β), and pol η during base excision repair. We then determined the efficiency of cdA incorporation by the polymerases using steady-state kinetics. We found that pol β and pol η incorporated cdAs opposite dT and dC with low efficiency, and incorporated cdAs were readily extended and ligated into duplex DNA. Using molecular docking analysis, we found that the 5',8-covalent bond in cdA disrupted its hydrogen bonding with a template base suggesting that the phosphodiester bond between the 3'-terminus nucleotide and the α-phosphate of cdATP were generated in the absence of hydrogen bonding. The enzyme kinetics analysis further suggests that pol β and pol η increased their substrate binding to facilitate the enzyme catalysis for cdA incorporation. Our study reveals unique mechanisms underlying the accumulation of cdPu lesions in the genome resulting from nucleotide incorporation by repair DNA polymerases.
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Affiliation(s)
- Pawlos S. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Daniela Hernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Christopher Brache
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | | | - Marios G. Krokidis
- Institute of Nanoscience and Nanotechnology, N.C.S.R. “Demokritos,” 15341, Agia Paraskevi, Athens, Greece
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL, USA,Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA,Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA,Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA,Correspondence:
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18
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Rocha K, Magallon J, Reeves C, Phan K, Vu P, Oakley-Havens CL, Kwan S, Ramirez MS, LaVoi T, Donow H, Chapagain P, Santos R, Pinilla C, Giulianotti MA, Tolmasky ME. Inhibition of Aminoglycoside 6'- N-acetyltransferase Type Ib (AAC(6')-Ib): Structure-Activity Relationship of Substituted Pyrrolidine Pentamine Derivatives as Inhibitors. Biomedicines 2021; 9:biomedicines9091218. [PMID: 34572404 PMCID: PMC8471502 DOI: 10.3390/biomedicines9091218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
The aminoglycoside 6'-N-acetyltransferase type Ib (AAC(6')-Ib) is a common cause of resistance to amikacin and other aminoglycosides in Gram-negatives. Utilization of mixture-based combinatorial libraries and application of the positional scanning strategy identified an inhibitor of AAC(6')-Ib. This inhibitor's chemical structure consists of a pyrrolidine pentamine scaffold substituted at four locations (R1, R3, R4, and R5). The substituents are two S-phenyl groups (R1 and R4), an S-hydroxymethyl group (R3), and a 3-phenylbutyl group (R5). Another location, R2, does not have a substitution, but it is named because its stereochemistry was modified in some compounds utilized in this study. Structure-activity relationship (SAR) analysis using derivatives with different functionalities, modified stereochemistry, and truncations was carried out by assessing the effect of the addition of each compound at 8 µM to 16 µg/mL amikacin-containing media and performing checkerboard assays varying the concentrations of the inhibitor analogs and the antibiotic. The results show that: (1) the aromatic functionalities at R1 and R4 are essential, but the stereochemistry is essential only at R4; (2) the stereochemical conformation at R2 is critical; (3) the hydroxyl moiety at R3 as well as stereoconformation are required for full inhibitory activity; (4) the phenyl functionality at R5 is not essential and can be replaced by aliphatic groups; (5) the location of the phenyl group on the butyl carbon chain at R5 is not essential; (6) the length of the aliphatic chain at R5 is not critical; and (7) all truncations of the scaffold resulted in inactive compounds. Molecular docking revealed that all compounds preferentially bind to the kanamycin C binding cavity, and binding affinity correlates with the experimental data for most of the compounds evaluated. The SAR results in this study will serve as the basis for the design of new analogs in an effort to improve their ability to induce phenotypic conversion to susceptibility in amikacin-resistant pathogens.
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Affiliation(s)
- Kenneth Rocha
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (K.R.); (J.M.); (C.R.); (K.P.); (P.V.); (C.L.O.-H.); (S.K.); (M.S.R.)
| | - Jesus Magallon
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (K.R.); (J.M.); (C.R.); (K.P.); (P.V.); (C.L.O.-H.); (S.K.); (M.S.R.)
| | - Craig Reeves
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (K.R.); (J.M.); (C.R.); (K.P.); (P.V.); (C.L.O.-H.); (S.K.); (M.S.R.)
| | - Kimberly Phan
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (K.R.); (J.M.); (C.R.); (K.P.); (P.V.); (C.L.O.-H.); (S.K.); (M.S.R.)
| | - Peter Vu
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (K.R.); (J.M.); (C.R.); (K.P.); (P.V.); (C.L.O.-H.); (S.K.); (M.S.R.)
| | - Crista L. Oakley-Havens
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (K.R.); (J.M.); (C.R.); (K.P.); (P.V.); (C.L.O.-H.); (S.K.); (M.S.R.)
| | - Stella Kwan
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (K.R.); (J.M.); (C.R.); (K.P.); (P.V.); (C.L.O.-H.); (S.K.); (M.S.R.)
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (K.R.); (J.M.); (C.R.); (K.P.); (P.V.); (C.L.O.-H.); (S.K.); (M.S.R.)
| | - Travis LaVoi
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA; (T.L.); (H.D.); (C.P.); (M.A.G.)
| | - Haley Donow
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA; (T.L.); (H.D.); (C.P.); (M.A.G.)
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA;
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Radleigh Santos
- Department of Mathematics, Nova Southeastern University, Fort Lauderdale, FL 33314, USA;
| | - Clemencia Pinilla
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA; (T.L.); (H.D.); (C.P.); (M.A.G.)
| | - Marc A. Giulianotti
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA; (T.L.); (H.D.); (C.P.); (M.A.G.)
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (K.R.); (J.M.); (C.R.); (K.P.); (P.V.); (C.L.O.-H.); (S.K.); (M.S.R.)
- Correspondence: ; Tel.: +1-657-278-5263
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Heath LC, Tiwari P, Sadhukhan B, Tiwari S, Chapagain P, Xu T, Li G, Joshi B, Yan J. Building climate change resilience by using a versatile toolkit for local governments and communities in rural Himalaya. Environ Res 2020; 188:109636. [PMID: 32599389 DOI: 10.1016/j.envres.2020.109636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
With the impacts of climate disruption becoming more evident there has been an increase in the uptake of climate change adaptation "toolkits" to assist local governments build community resilience and adapt to the impacts of climate change. There is increasing attention and call for practitioners to adopt proactive and participatory approaches to help in the adaptive response planning process. One such toolkit is the International Council for Local Environmental Initiatives (ICLEI) Asian Cities Climate Change Resilience Network (ACCRN) Process (IAP). This is a simple but rigorous toolkit developed to help local governments in Asian cities build resilience to the impacts of climate change. This paper outlines the application of the toolkit to determine its versatility in the rural context and was trialled in the Himalayan rural enclave of Ramgad in the Indian state of Uttarakhand. Given the differences between urban and rural environments, the outcomes highlighted the need for further investigation and analysis into the process to ensure that the methodology truly reflects the nature of rural systems and their level of vulnerability and adaptive capacity. Overall, the toolkit proved to be a simple but versatile toolkit to assess the vulnerability and adaptive capacity of communities in rural Himalaya. Over 40 resilience intervention strategies were developed for the Ramgad enclave and these were prioritized according to their technical, political, social and economic feasibility.
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Affiliation(s)
- Lance C Heath
- Australian National University, Fenner School of Society & Environment Building 141, Linnaeus Way, Acton, Canberra, ACT, 0200; Sustineo Pty Ltd, 1b/32 Thesiger Court, Braddon, Canberra, ACT, 2612 Australia; Freelance Solutions, 37 Loftus St, Yarralumla, Canberra, ACT, 2600, Australia.
| | | | - Bedoshruti Sadhukhan
- ICLEI, Local Governments for Sustainability South Asia C-3 Green Park Extension, New Delhi, India.
| | - Sunandan Tiwari
- ICLEI, World Secretariat, Kaiser-Friedrich-Strasse 7 D-53113 Bonn, Germany New Delhi, India.
| | | | - Tingbao Xu
- Australian National University, Fenner School of Society & Environment Building 141, Linnaeus Way, Acton, Canberra, ACT, 0200.
| | - Geraldine Li
- Australian National University, Fenner School of Society & Environment Building 141, Linnaeus Way, Acton, Canberra, ACT, 0200.
| | - Bhagwati Joshi
- Government Post Graduate College, Rudrapur 263153, India.
| | - Jianzhong Yan
- Southwest University, Beibei District, Chongqing, China.
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20
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Beddingfield B, Iwanaga N, Chapagain P, Zheng W, Roy CJ, Hu TY, Kolls J, Bix G. The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection. bioRxiv 2020. [PMID: 32587959 DOI: 10.1101/2020.06.15.153387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Many efforts to design and screen therapeutics for severe acute respiratory syndrome coronavirus (SARS-CoV-2) have focused on inhibiting viral cell entry by disrupting ACE2 binding with the SARS-CoV-2 spike protein. This work focuses on inhibiting SARS-CoV-2 entry through a hypothesized α5β1 integrin-based mechanism, and indicates that inhibiting the spike protein interaction with α5β1 integrin (+/- ACE2), and the interaction between α5β1 integrin and ACE2 using a molecule ATN-161 represents a promising approach to treat COVID-19.
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Pokhrel R, Chapagain P, Siltberg-Liberles J. Potential RNA-dependent RNA polymerase inhibitors as prospective therapeutics against SARS-CoV-2. J Med Microbiol 2020; 69:864-873. [PMID: 32469301 PMCID: PMC7451031 DOI: 10.1099/jmm.0.001203] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/27/2020] [Indexed: 01/13/2023] Open
Abstract
Introduction. The emergence of SARS-CoV-2 has taken humanity off guard. Following an outbreak of SARS-CoV in 2002, and MERS-CoV about 10 years later, SARS-CoV-2 is the third coronavirus in less than 20 years to cross the species barrier and start spreading by human-to-human transmission. It is the most infectious of the three, currently causing the COVID-19 pandemic. No treatment has been approved for COVID-19. We previously proposed targets that can serve as binding sites for antiviral drugs for multiple coronaviruses, and here we set out to find current drugs that can be repurposed as COVID-19 therapeutics.Aim. To identify drugs against COVID-19, we performed an in silico virtual screen with the US Food and Drug Administration (FDA)-approved drugs targeting the RNA-dependent RNA polymerase (RdRP), a critical enzyme for coronavirus replication.Methodology. Initially, no RdRP structure of SARS-CoV-2 was available. We performed basic sequence and structural analysis to determine if RdRP from SARS-CoV was a suitable replacement. We performed molecular dynamics simulations to generate multiple starting conformations that were used for the in silico virtual screen. During this work, a structure of RdRP from SARS-CoV-2 became available and was also included in the in silico virtual screen.Results. The virtual screen identified several drugs predicted to bind in the conserved RNA tunnel of RdRP, where many of the proposed targets were located. Among these candidates, quinupristin is particularly interesting because it is expected to bind across the RNA tunnel, blocking access from both sides and suggesting that it has the potential to arrest viral replication by preventing viral RNA synthesis. Quinupristin is an antibiotic that has been in clinical use for two decades and is known to cause relatively minor side effects.Conclusion. Quinupristin represents a potential anti-SARS-CoV-2 therapeutic. At present, we have no evidence that this drug is effective against SARS-CoV-2 but expect that the biomedical community will expeditiously follow up on our in silico findings.
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Affiliation(s)
- Rudramani Pokhrel
- Department of Physics, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
| | - Jessica Siltberg-Liberles
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
- Department of Biological Sciences, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
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22
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Porter JE, Chapagain P, Fernandez-Lima F. Single-stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formation. Rapid Commun Mass Spectrom 2019; 33 Suppl 2:60-65. [PMID: 30506977 DOI: 10.1002/rcm.8367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
RATIONALE DNA quadruplex structures have emerged as novel drug targets due to their role in preventing abnormal gene transcription and maintaining telomere stability. Trapped Ion Mobility Spectrometry-Mass Spectrometry (TIMS-MS), combined with theoretical modeling, is a powerful tool for studying the kinetic intermediates of DNA complexes formed in solution and interrogated in the gas phase after desolvation. METHODS A TAGGGT ssDNA sequence was purchased and studied in 10 mM ammonium acetate using nanospray electrospray ionization (nESI)-TIMS-MS in positive and negative ion mode. Collisional cross section (CCS) profiles were measured using internal calibration (Tune Mix). Theoretical structures were proposed based on molecular dynamics, charge location and geometry optimization for the most intense IMS bands based on the number of TAGGGT units, adduct form and charge states. RESULTS A distribution of monomeric, dimeric and tetrameric TAGGGT structures were formed in solution and separated in the gas phase based on their mobility and m/z value (e.g., [M + 2H]+2 , [2M + 3H]+3 , [M - 2H]-2 , [2M - 3H]-3 , [4M + 4H]+4 , [4M + 3H + NH4 ]+4 , [4M + 2H + 2NH4 ]+4 and [4M + H + 3NH4 ]+4 ). The high mobility resolution of the TIMS-MS analyzer permitted the observation of multiple CCS bands per molecular ion form. Comparison with theoretical candidate structures suggests that monomeric TAGGGT species are stabilized by A-T and G+ -G interactions, with the size of the conformer influenced by the proton location. In the case of the TAGGGT quadruplex, the protonated species displayed a broad CCS distribution, while six discrete conformers were stabilized by the presence of ammonium ions (n = 1-3). CONCLUSIONS This is the first observation of multiple conformations of TAGGGT complexes (n = 1, 2 and 4) in 10 mM ammonium acetate. Candidate structures with intramolecular interactions of the form of G+ -G and traditional A-T base pairing agreed with the experimental trends. Our results demonstrate the structural diversity of TAGGGT monomers, dimers and tetramers in the gas phase beyond the previously reported solution structure, using 10 mM ammonium acetate to replicate biological conditions.
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Affiliation(s)
- Jacob E Porter
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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23
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Dhakal C, Chapagain P, Wang X. Temperature Dependence of the Protein-Chromophore Hydrogen Bond Dynamics in the Far-Red Fluorescent Proteins mNeptune1, mNeptune2.5 and mCardinal2. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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24
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Wang L, Feng Y, Yan D, Qin L, Grati M, Mittal R, Li T, Sundhari AK, Liu Y, Chapagain P, Blanton SH, Liao S, Liu X. A dominant variant in the PDE1C gene is associated with nonsyndromic hearing loss. Hum Genet 2018; 137:437-446. [PMID: 29860631 PMCID: PMC6560636 DOI: 10.1007/s00439-018-1895-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/26/2018] [Indexed: 01/02/2023]
Abstract
Identification of genes with variants causing non-syndromic hearing loss (NSHL) is challenging due to genetic heterogeneity. The difficulty is compounded by technical limitations that in the past prevented comprehensive gene identification. Recent advances in technology, using targeted capture and next-generation sequencing (NGS), is changing the face of gene identification and making it possible to rapidly and cost-effectively sequence the whole human exome. Here, we characterize a five-generation Chinese family with progressive, postlingual autosomal dominant nonsyndromic hearing loss (ADNSHL). By combining population-specific mutation arrays, targeted deafness genes panel, whole exome sequencing (WES), we identified PDE1C (Phosphodiesterase 1C) c.958G>T (p.A320S) as the disease-associated variant. Structural modeling insights into p.A320S strongly suggest that the sequence alteration will likely affect the substrate-binding pocket of PDE1C. By whole-mount immunofluorescence on postnatal day 3 mouse cochlea, we show its expression in outer (OHC) and inner (IHC) hair cells cytosol co-localizing with Lamp-1 in lysosomes. Furthermore, we provide evidence that the variant alters the PDE1C hydrolytic activity for both cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP). Collectively, our findings indicate that the c.958G>T variant in PDE1C may disrupt the cross talk between cGMP-signaling and cAMP pathways in Ca2+ homeostasis.
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Affiliation(s)
- Li Wang
- Institute of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
- Department of Otolaryngology (D-48), Miller School of Medicine, University of Miami, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, China
| | - Denise Yan
- Department of Otolaryngology (D-48), Miller School of Medicine, University of Miami, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Litao Qin
- Institute of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - M'hamed Grati
- Department of Otolaryngology (D-48), Miller School of Medicine, University of Miami, 1666 NW 12th Avenue, Miami, FL, 33136, USA
- Laboratory of Cell Structure and Dynamics, NIDCD, NIH, Bethesda, MD, 20892, USA
| | - Rahul Mittal
- Department of Otolaryngology (D-48), Miller School of Medicine, University of Miami, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Tao Li
- Institute of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Abhiraami Kannan Sundhari
- Department of Otolaryngology (D-48), Miller School of Medicine, University of Miami, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Yalan Liu
- Department of Otolaryngology (D-48), Miller School of Medicine, University of Miami, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Susan H Blanton
- Department of Otolaryngology (D-48), Miller School of Medicine, University of Miami, 1666 NW 12th Avenue, Miami, FL, 33136, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Shixiu Liao
- Institute of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Xuezhong Liu
- Department of Otolaryngology (D-48), Miller School of Medicine, University of Miami, 1666 NW 12th Avenue, Miami, FL, 33136, USA.
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, China.
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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25
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Butcher D, Chapagain P, Leng F, Fernandez-Lima F. Differentiating Parallel and Antiparallel DNA Duplexes in the Gas Phase Using Trapped Ion Mobility Spectrometry. J Phys Chem B 2018; 122:6855-6861. [PMID: 29886735 DOI: 10.1021/acs.jpcb.7b12544] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deoxyribonucleic acids can form a wide variety of structural motifs which differ greatly from the typical antiparallel duplex stabilized by Watson-Crick base pairing. Many of these structures are thought to occur in vivo and may have essential roles in the biology of the cell. Among these is the parallel-stranded duplex-a structural motif in which DNA strands associate in a head-to-head fashion with the 5' ends at the same end of the duplex-which is stabilized by reverse Watson-Crick base pairing. In this study, parallel- and antiparallel-stranded DNA duplexes formed from two different 12-mer oligonucleotides were studied using native electrospray ionization combined with trapped ion mobility spectrometry and mass spectrometry. The DNA duplex charge plays an important role in the gas-phase mobility profile, with a more compact form in negative mode than in positive mode (ΔΩ ≈ 100 Å2 between -4 and +4). Despite sequence mismatches, homo- and hetero-DNA duplexes were formed in solution and transfer to the gas phase, where a more compact structure was observed for the parallel compared to the antiparallel duplexes (ΔΩ ≈ 50 Å2), in good agreement with theoretical calculations. Theoretical studies suggest that a reduction (or compaction) along the helical axis of the parallel and antiparallel DNA duplexes is observed upon transfer to the gas phase.
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26
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Li W, Sun J, Ling J, Li J, He C, Liu Y, Chen H, Men M, Niu Z, Deng Y, Li M, Li T, Wen J, Sang S, Li H, Wan Z, Richard EM, Chapagain P, Yan D, Liu XZ, Mei L, Feng Y. ELMOD3, a novel causative gene, associated with human autosomal dominant nonsyndromic and progressive hearing loss. Hum Genet 2018; 137:329-342. [PMID: 29713870 DOI: 10.1007/s00439-018-1885-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/16/2018] [Indexed: 11/26/2022]
Abstract
Autosomal dominant nonsyndromic hearing loss (ADNSHL) is a highly genetically heterogeneous disorder. Up to date only approximately 37 ADNSHL-causing genes have been identified. The goal of this study was to determine the causative gene in a five-generation Chinese family with ADNSHL. A Chinese family was ascertained. Simultaneously, two affected individuals and one normal hearing control from the family were analyzed by whole exome capture sequencing. To assess the functional effect of the identified variant, in-vitro studies were performed. novel missense variant, c.512A>G (p.His171Arg) in exon 8 of the ELMO domain-containing 3 (ELMOD3) gene, was identified as a causative variant in this family affected by late-onset and progressive ADNSHL. The variant was validated by Sanger sequencing and found to co-segregate with the phenotype within the pedigree and was absent in 500 ethnically matched unrelated normal hearing control subjects. To our knowledge, this is the first report of a family with ADNSHL caused by ELMOD3 mutation. Western blots and immunofluorescence staining demonstrated that p.His171Arg resulted in abnormal expression levels of ELMOD3 and abnormal subcellular localization. Furthermore, the analysis of the stability of the wild-type (WT) and mutant ELMOD3 protein shows that the decay of p.His171Arg is faster than that of the WT, suggesting a shorter halflife of the c.512A > G variant. A novel variant in the ELMOD3 gene, encoding a member of the engulfment and cell motility (ELMO) family of GTPase-activating proteins, was identified for the first time as responsible for ADNSHL.
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Affiliation(s)
- Wu Li
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Jie Sun
- Department of Otolaryngology, The Eight Affiliated Hospital, Sun Yat-sen University, 3025 Shennan Middle Road, Shenzhen, Guangdong, China
| | - Jie Ling
- Institute of Precision Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
| | - Jiada Li
- Center for Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan, China
- School of Life Sciences, Central South University of China, 110 Xiangya Road, Changsha, Hunan, China
| | - Chufeng He
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Yalan Liu
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Hongsheng Chen
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Meichao Men
- Health Management Center, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
| | - Zhijie Niu
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Yuyuan Deng
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Meng Li
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Taoxi Li
- Center for Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan, China
- School of Life Sciences, Central South University of China, 110 Xiangya Road, Changsha, Hunan, China
| | - Jie Wen
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Shushan Sang
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China
| | - Haibo Li
- Department of Ophthalmology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
| | - Zhengqing Wan
- Center for Medical Genetics, Central South University, 110 Xiangya Road, Changsha, Hunan, China
- School of Life Sciences, Central South University of China, 110 Xiangya Road, Changsha, Hunan, China
| | - Elodie M Richard
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, Florida, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, USA
| | - Xue Zhong Liu
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Lingyun Mei
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China.
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China.
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, China.
- Province Key Laboratory of Otolaryngology Critical Diseases, Changsha, Hunan, China.
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27
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Wang L, Yan D, Qin L, Li T, Liu H, Li W, Mittal R, Yong F, Chapagain P, Liao S, Liu X. Amino acid 118 in the Deafness Causing (DFNA20/26) ACTG1 gene is a Mutational Hot Spot. Gene Rep 2018; 11:264-269. [PMID: 30599039 DOI: 10.1016/j.genrep.2018.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background Hearing loss is an economically and socially important cause of human morbidity, affecting 360 million people (over 5% of the world's population), of whom 32 million are children. Of the estimated minimum of 50% of hereditary hearing loss, non-syndromic hearing loss (NSHL) accounts for more than 70%. The autosomal dominant non-syndromic hearing loss (ADNSHL) is highly heterogeneous. To date, 67 ADNSHL loci (DFNA1-67) have been mapped; however, only 35 causative genes have been cloned since 1997 (http://hereditaryhearingloss.org/). Methods To identify the genetic basis of hereditary hearing loss in a Chinese family with ADNSHL, we undertook a targeted sequencing of 180 genes using a custom capture panel (MiamiOtoGenes). Results The onset of hearing loss in the family occurred between the ages of 15 and 18 years. Hearing loss was bilateral, started in the high frequency and progressed to lower frequencies. The c.353A>T (K118M) in the AC TG1 gene was identified by panel and was confirmed by Sanger sequencing and was present in all affected family members. So far, five of the 23 DFNA20/26 families worldwide have been found to carry mutation involving the residue K118. Conclusions This is the first report of K118M mutation in the ACTG1 gene causing hearing loss in the Chinese population. The present data are in line with previous evidence to suggest that codon K118 of ACTG1 may represent a mutational hot spot that justifies a mutation screen for diagnostic purpose in the genetically heterogeneous group of DFNA20/26.
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Affiliation(s)
- Li Wang
- Institute of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, USA
| | - Litao Qin
- Institute of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Tao Li
- Institute of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongjian Liu
- Department of Otorhinolaryngology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Wan Li
- Department of Otorhinolaryngology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Rahul Mittal
- Institute of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng Yong
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, China
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, Florida.,Biomolecular Sciences Institute, Florida International University, Miami, Florida
| | - Shixiu Liao
- Institute of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, USA
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Mittal R, Patel AP, Nguyen D, Pan DR, Jhaveri VM, Rudman JR, Dharmaraja A, Yan D, Feng Y, Chapagain P, Lee DJ, Blanton SH, Liu XZ. Genetic basis of hearing loss in Spanish, Hispanic and Latino populations. Gene 2018; 647:297-305. [PMID: 29331482 PMCID: PMC5806531 DOI: 10.1016/j.gene.2018.01.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/02/2018] [Accepted: 01/06/2018] [Indexed: 12/13/2022]
Abstract
Hearing loss (HL) is the most common neurosensory disorder affecting humans. The screening, prevention and treatment of HL require a better understanding of the underlying molecular mechanisms. Genetic predisposition is one of the most common factors that leads to HL. Most HL studies include few Spanish, Hispanic and Latino participants, leaving a critical gap in our understanding about the prevalence, impact, unmet health care needs, and genetic factors associated with hearing impairment among Spanish, Hispanic and Latino populations. The few studies which have been performed show that the gene variants commonly associated with HL in non-Spanish and non-Hispanic populations are infrequently responsible for hearing impairment in Spanish as well as Hispanic and Latino populations (hereafter referred to as Hispanic). To design effective screening tools to detect HL in Spanish and Hispanic populations, studies must be conducted to determine the gene variants that are most commonly associated with hearing impairment in this racial/ethnic group. In this review article, we summarize gene variants and loci associated with HL in Spanish and Hispanic populations. Identifying new genetic variants associated with HL in Spanish and Hispanic populations will pave the way to develop effective screening tools and therapeutic strategies for HL.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Amit P Patel
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Desiree Nguyen
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Debbie R Pan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Vasanti M Jhaveri
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason R Rudman
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Arjuna Dharmaraja
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, China
| | - Prem Chapagain
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - David J Lee
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan H Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, China; Tsinghua University School of Medicine, Beijing 10084, China; Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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29
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Tiwari P, Chapagain P, Tse-Dinh YC, Uren A. Covalent Complex Model of DNA Topoisomerase and DNA for Molecular Dynamics Simulation. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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30
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Mittal R, Nguyen D, Debs LH, Patel AP, Liu G, Jhaveri VM, S. Kay SI, Mittal J, Bandstra ES, Younis RT, Chapagain P, Jayaweera DT, Liu XZ. Zika Virus: An Emerging Global Health Threat. Front Cell Infect Microbiol 2017; 7:486. [PMID: 29276699 PMCID: PMC5727043 DOI: 10.3389/fcimb.2017.00486] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/13/2017] [Indexed: 01/07/2023] Open
Abstract
Zika virus (ZIKV) is an emerging healthcare threat. The presence of the mosquito Aedes species across South and Central America in combination with complementary climates have incited an epidemic of locally transmitted cases of ZIKV infection in Brazil. As one of the most significant current public health concerns in the Americas, ZIKV epidemic has been a cause of alarm due to its known and unknown complications. At this point, there has been a clear association between ZIKV infection and severe clinical manifestations in both adults and neonates, including but not limited to neurological deficits such as Guillain-Barré syndrome (GBS) and microcephaly, respectively. The gravity of the fetal anomalies linked to ZIKV vertical transmission from the mother has prompted a discussion on whether to include ZIKV as a formal member of the TORCH [Toxoplasma gondii, other, rubella virus, cytomegalovirus (CMV), and herpes] family of pathogens known to breach placental barriers and cause congenital disease in the fetus. The mechanisms of these complex phenotypes have yet to be fully described. As such, diagnostic tools are limited and no effective modalities are available to treat ZIKV. This article will review the recent advancements in understanding the pathogenesis of ZIKV infection as well as diagnostic tests available to detect the infection. Due to the increase in incidence of ZIKV infections, there is an immediate need to develop new diagnostic tools and novel preventive as well as therapeutic modalities based on understanding the molecular mechanisms underlying the disease.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States,*Correspondence: Rahul Mittal
| | - Desiree Nguyen
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Luca H. Debs
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Amit P. Patel
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - George Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Vasanti M. Jhaveri
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Sae-In S. Kay
- Department of Surgery, Division of Otorhinolaryngology, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Jeenu Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Emmalee S. Bandstra
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Ramzi T. Younis
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States,Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States,Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Prem Chapagain
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, FL, United States
| | - Dushyantha T. Jayaweera
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States,Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States,Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States,Xue Zhong Liu
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31
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Tiwari P, Chapagain P, Banda S, Darici Y, Tse-Dinh YC, Üren A. Exploring Molecular Interactions between Escherichia coli RNA Polymerase and Topoisomerase I by Molecular Simulations. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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32
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Peña-Flores NL, Uzcategui C, Steckmann T, Chapagain P, Gerstman B. Temperature Dependent Pair-Wise Amino Acid Structural Propensity in ccβ and Implications for α to β Secondary Structural Conversion. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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33
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Mittal R, Aranke M, Debs LH, Nguyen D, Patel AP, Grati M, Mittal J, Yan D, Chapagain P, Eshraghi AA, Liu XZ. Indispensable Role of Ion Channels and Transporters in the Auditory System. J Cell Physiol 2016; 232:743-758. [DOI: 10.1002/jcp.25631] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 09/30/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Mayank Aranke
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Luca H. Debs
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Desiree Nguyen
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Amit P. Patel
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - M'hamed Grati
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Jeenu Mittal
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Denise Yan
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Prem Chapagain
- Department of Physics; Florida International University; Miami Florida
- Biomolecular Science Institute; Florida International University; Miami Florida
| | - Adrien A. Eshraghi
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Xue Zhong Liu
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
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34
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Mittal R, Chan B, Grati M, Mittal J, Patel K, Debs LH, Patel AP, Yan D, Chapagain P, Liu XZ. Cover Image, Volume 231, Number 8, August 2016. J Cell Physiol 2016. [DOI: 10.1002/jcp.25403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Brandon Chan
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - M'hamed Grati
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Jeenu Mittal
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Kunal Patel
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Luca H. Debs
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Amit P. Patel
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Denise Yan
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Prem Chapagain
- Department of Physics; Florida International University; Miami Florida
- Biomolecular Science Institute; Florida International University; Miami Florida
| | - Xue Zhong Liu
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
- Department of Human Genetics; University of Miami Miller School of Medicine; Miami Florida
- Department of Biochemistry; University of Miami Miller School of Medicine; Miami Florida
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35
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Mittal R, Patel AP, Debs LH, Nguyen D, Patel K, Grati M, Mittal J, Yan D, Chapagain P, Liu XZ. Intricate Functions of Matrix Metalloproteinases in Physiological and Pathological Conditions. J Cell Physiol 2016; 231:2599-621. [DOI: 10.1002/jcp.25430] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Amit P. Patel
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Luca H. Debs
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Desiree Nguyen
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Kunal Patel
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - M'hamed Grati
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Jeenu Mittal
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Denise Yan
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
| | - Prem Chapagain
- Department of Physics; Florida International University; Miami Florida
- Biomolecular Science Institute; Florida International University; Miami Florida
| | - Xue Zhong Liu
- Department of Otolaryngology; University of Miami Miller School of Medicine; Miami Florida
- Department of Biochemistry; University of Miami Miller School of Medicine; Miami Florida
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36
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Mittal R, Grati M, Sedlacek M, Yuan F, Chang Q, Yan D, Lin X, Kachar B, Farooq A, Chapagain P, Zhang Y, Liu XZ. Characterization of ATPase Activity of P2RX2 Cation Channel. Front Physiol 2016; 7:186. [PMID: 27252659 PMCID: PMC4878533 DOI: 10.3389/fphys.2016.00186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/09/2016] [Indexed: 12/31/2022] Open
Abstract
P2X purinergic receptors are plasma membrane ATP-dependent cation channels that are broadly distributed in the mammalian tissues. P2RX2 is a modulator of auditory sensory hair cell mechanotransduction and plays an important role in hair cell tolerance to noise. In this study, we demonstrate for the first time in vitro and in cochlear neuroepithelium, that P2RX2 possesses the ATPase activity. We observed that the P2RX2 V60L human deafness mutation alters its ability to bind ATP, while the G353R has no effect on ATP binding or hydrolysis. A non-hydrolysable ATP assay using HEK293 cells suggests that ATP hydrolysis plays a significant role in the opening and gating of the P2RX2 ion channel. Moreover, the results of structural modeling of the molecule was in agreement with our experimental observations. These novel findings suggest the intrinsic ATPase activity of P2RX2 and provide molecular insights into the channel opening.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine Miami, FL, USA
| | - M'hamed Grati
- Department of Otolaryngology, University of Miami Miller School of Medicine Miami, FL, USA
| | - Miloslav Sedlacek
- Laboratory of Cell Structure and Dynamics, Section on Structural Cell Biology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health Bethesda, MD, USA
| | - Fenghua Yuan
- Department of Biochemistry, University of Miami Leonard M. Miller School of Medicine Miami, FL, USA
| | - Qing Chang
- Department of Otolaryngology, Emory University Atlanta, GA, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine Miami, FL, USA
| | - Xi Lin
- Department of Otolaryngology, Emory University Atlanta, GA, USA
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, Section on Structural Cell Biology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health Bethesda, MD, USA
| | - Amjad Farooq
- Department of Biochemistry, University of Miami Leonard M. Miller School of Medicine Miami, FL, USA
| | - Prem Chapagain
- Department of Physics, Florida International University Miami, FL, USA
| | - Yanbin Zhang
- Department of Biochemistry, University of Miami Leonard M. Miller School of Medicine Miami, FL, USA
| | - Xue Z Liu
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, USA; Department of Biochemistry, University of Miami Leonard M. Miller School of MedicineMiami, FL, USA; Department of Otolaryngology, Central South University, Xiangya HospitalChangsha, China
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37
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Fulcrand G, Chapagain P, Dunlap D, Leng F. Direct observation of a 91 bp LacI-mediated, negatively supercoiled DNA loop by atomic force microscope. FEBS Lett 2016; 590:613-8. [PMID: 26878689 DOI: 10.1002/1873-3468.12094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/04/2016] [Accepted: 02/09/2016] [Indexed: 01/08/2023]
Abstract
Escherichia coli lactose repressor (LacI), a tetrameric protein, is a paradigmatic transcriptional factor that controls the expression of lacZYA in the lac operon. It specifically binds to the O1, O2, and O3 operators of the lac promoter, forms DNA loops, and regulates transcription of the lac operon. In this article, utilizing combined techniques of DNA-nicking assay and AFM imaging, we directly observed a 91 bp LacI-mediated, negatively supercoiled DNA loop mimicking the DNA loop between the O1 and O3 operators in the lac promoter.
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Affiliation(s)
- Geraldine Fulcrand
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.,Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| | - Prem Chapagain
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.,Department of Physics, Florida International University, Miami, FL, USA
| | - David Dunlap
- Department of Physics, Emory University, Atlanta, GA, USA
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.,Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
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38
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Chapagain P, Regmi C, Gerstman B. On the Origin of the Extended Stoke's Shifts in Fluorescent Proteins. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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39
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Fulcrand G, Dages S, Zhi X, Chapagain P, Gerstman BS, Dunlap D, Leng F. DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli. Sci Rep 2016; 6:19243. [PMID: 26763930 PMCID: PMC4725879 DOI: 10.1038/srep19243] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/10/2015] [Indexed: 12/20/2022] Open
Abstract
Escherichia coli lac repressor (LacI) is a paradigmatic transcriptional factor that controls the expression of lacZYA in the lac operon. This tetrameric protein specifically binds to the O1, O2 and O3 operators of the lac operon and forms a DNA loop to repress transcription from the adjacent lac promoter. In this article, we demonstrate that upon binding to the O1 and O2 operators at their native positions LacI constrains three (−) supercoils within the 401-bp DNA loop of the lac promoter and forms a topological barrier. The stability of LacI-mediated DNA topological barriers is directly proportional to its DNA binding affinity. However, we find that DNA supercoiling modulates the basal expression from the lac operon in E. coli. Our results are consistent with the hypothesis that LacI functions as a topological barrier to constrain free, unconstrained (−) supercoils within the 401-bp DNA loop of the lac promoter. These constrained (−) supercoils enhance LacI’s DNA-binding affinity and thereby the repression of the promoter. Thus, LacI binding is superhelically modulated to control the expression of lacZYA in the lac operon under varying growth conditions.
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Affiliation(s)
- Geraldine Fulcrand
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Chemistry &Biochemistry, Florida International University, Miami, FL 33199
| | - Samantha Dages
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Chemistry &Biochemistry, Florida International University, Miami, FL 33199
| | - Xiaoduo Zhi
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Chemistry &Biochemistry, Florida International University, Miami, FL 33199
| | - Prem Chapagain
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Physics, Florida International University, Miami, FL 33199
| | - Bernard S Gerstman
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Physics, Florida International University, Miami, FL 33199
| | - David Dunlap
- Department of Physics, Emory University, Atlanta, GA 30322
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Chemistry &Biochemistry, Florida International University, Miami, FL 33199
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40
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Mittal R, Chan B, Grati M, Mittal J, Patel K, Debs LH, Patel AP, Yan D, Chapagain P, Liu XZ. Molecular Structure and Regulation of P2X Receptors With a Special Emphasis on the Role of P2X2 in the Auditory System. J Cell Physiol 2015; 231:1656-70. [PMID: 26627116 DOI: 10.1002/jcp.25274] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 12/01/2015] [Indexed: 12/23/2022]
Abstract
The P2X purinergic receptors are cation-selective channels gated by extracellular adenosine 5'-triphosphate (ATP). These purinergic receptors are found in virtually all mammalian cell types and facilitate a number of important physiological processes. Within the past few years, the characterization of crystal structures of the zebrafish P2X4 receptor in its closed and open states has provided critical insights into the mechanisms of ligand binding and channel activation. Understanding of this gating mechanism has facilitated to design and interpret new modeling and structure-function experiments to better elucidate how different agonists and antagonists can affect the receptor with differing levels of potency. This review summarizes the current knowledge on the structure, activation, allosteric modulators, function, and location of the different P2X receptors. Moreover, an emphasis on the P2X2 receptors has been placed in respect to its role in the auditory system. In particular, the discovery of three missense mutations in P2X2 receptors could become important areas of study in the field of gene therapy to treat progressive and noise-induced hearing loss. J. Cell. Physiol. 231: 1656-1670, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Brandon Chan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - M'hamed Grati
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Jeenu Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Kunal Patel
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Luca H Debs
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Amit P Patel
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, Florida.,Biomolecular Science Institute, Florida International University, Miami, Florida
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida.,Department of Biochemistry, University of Miami Miller School of Medicine, Miami, Florida
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