51
|
Wuyun Q, Chen Y, Shen Y, Cao Y, Hu G, Cui W, Gao J, Zheng W. Recent Progress of Protein Tertiary Structure Prediction. Molecules 2024; 29:832. [PMID: 38398585 PMCID: PMC10893003 DOI: 10.3390/molecules29040832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The prediction of three-dimensional (3D) protein structure from amino acid sequences has stood as a significant challenge in computational and structural bioinformatics for decades. Recently, the widespread integration of artificial intelligence (AI) algorithms has substantially expedited advancements in protein structure prediction, yielding numerous significant milestones. In particular, the end-to-end deep learning method AlphaFold2 has facilitated the rise of structure prediction performance to new heights, regularly competitive with experimental structures in the 14th Critical Assessment of Protein Structure Prediction (CASP14). To provide a comprehensive understanding and guide future research in the field of protein structure prediction for researchers, this review describes various methodologies, assessments, and databases in protein structure prediction, including traditionally used protein structure prediction methods, such as template-based modeling (TBM) and template-free modeling (FM) approaches; recently developed deep learning-based methods, such as contact/distance-guided methods, end-to-end folding methods, and protein language model (PLM)-based methods; multi-domain protein structure prediction methods; the CASP experiments and related assessments; and the recently released AlphaFold Protein Structure Database (AlphaFold DB). We discuss their advantages, disadvantages, and application scopes, aiming to provide researchers with insights through which to understand the limitations, contexts, and effective selections of protein structure prediction methods in protein-related fields.
Collapse
Affiliation(s)
- Qiqige Wuyun
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Yihan Chen
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071, China;
| | - Yifeng Shen
- Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0882, Kanagawa, Japan;
| | - Yang Cao
- College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Gang Hu
- NITFID, School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin 300071, China
| | - Wei Cui
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071, China;
| | - Jianzhao Gao
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071, China;
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
52
|
Ruf M, Cunningham S, Wandersee A, Brox R, Achenbach S, Strobel J, Hackstein H, Schneider S. SERPINC1 c.1247dupC: a novel SERPINC1 gene mutation associated with familial thrombosis results in a secretion defect and quantitative antithrombin deficiency. Thromb J 2024; 22:19. [PMID: 38347553 PMCID: PMC10860291 DOI: 10.1186/s12959-024-00589-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Antithrombin (AT) is an important anticoagulant in hemostasis. We describe here the characterization of a novel AT mutation associated with clinically relevant thrombosis. A pair of sisters with confirmed type I AT protein deficiency was genetically analyzed on suspicion of an inherited SERPINC1 mutation. A frameshift mutation, c.1247dupC, was identified and the effect of this mutation was examined on the cellular and molecular level. METHODS Plasmids for the expression of wild-type (WT) and mutated SERPINC1 coding sequence (CDS) fused to green fluorescent protein (GFP) or hemagglutinin (HA) tag were transfected into HEK293T cells. Subcellular localization and secretion of the respective fusion proteins were analyzed by confocal laser scanning microscopy and Western blot. RESULTS The c.1247dupC mutation results in a frameshift in the CDS of the SERPINC1 gene and a subsequently altered amino acid sequence (p.Ser417LysfsTer48). This alteration affects the C-terminus of the AT antigen and results in impaired secretion as confirmed by GFP- and HA-tagged mutant AT analyzed in HEK293T cells. CONCLUSION The p.Ser417LysfsTer48 mutation leads to impaired secretion, thus resulting in a quantitative AT deficiency. This is in line with the type I AT deficiency observed in the patients.
Collapse
Affiliation(s)
- Maximilian Ruf
- Department of Transfusion Medicine and Hemostaseology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Krankenhausstr. 12, 91054, Erlangen, Germany
| | - Sarah Cunningham
- Department of Transfusion Medicine and Hemostaseology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Krankenhausstr. 12, 91054, Erlangen, Germany
| | - Alexandra Wandersee
- Department of Transfusion Medicine and Hemostaseology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Krankenhausstr. 12, 91054, Erlangen, Germany
| | - Regine Brox
- Department of Transfusion Medicine and Hemostaseology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Krankenhausstr. 12, 91054, Erlangen, Germany
| | - Susanne Achenbach
- Department of Transfusion Medicine and Hemostaseology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Krankenhausstr. 12, 91054, Erlangen, Germany
| | - Julian Strobel
- Department of Transfusion Medicine and Hemostaseology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Krankenhausstr. 12, 91054, Erlangen, Germany
| | - Holger Hackstein
- Department of Transfusion Medicine and Hemostaseology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Krankenhausstr. 12, 91054, Erlangen, Germany
| | - Sabine Schneider
- Department of Transfusion Medicine and Hemostaseology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Krankenhausstr. 12, 91054, Erlangen, Germany.
| |
Collapse
|
53
|
Tasneem A, Sultan A, Singh P, Bairagya HR, Almasoudi HH, Alhazmi AYM, Binshaya AS, Hakami MA, Alotaibi BS, Abdulaziz Eisa A, Alolaiqy ASI, Hasan MR, Dev K, Dohare R. Identification of potential therapeutic targets for COVID-19 through a structural-based similarity approach between SARS-CoV-2 and its human host proteins. Front Genet 2024; 15:1292280. [PMID: 38370514 PMCID: PMC10869566 DOI: 10.3389/fgene.2024.1292280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/08/2024] [Indexed: 02/20/2024] Open
Abstract
Background: The COVID-19 pandemic caused by SARS-CoV-2 has led to millions of deaths worldwide, and vaccination efficacy has been decreasing with each lineage, necessitating the need for alternative antiviral therapies. Predicting host-virus protein-protein interactions (HV-PPIs) is essential for identifying potential host-targeting drug targets against SARS-CoV-2 infection. Objective: This study aims to identify therapeutic target proteins in humans that could act as virus-host-targeting drug targets against SARS-CoV-2 and study their interaction against antiviral inhibitors. Methods: A structure-based similarity approach was used to predict human proteins similar to SARS-CoV-2 ("hCoV-2"), followed by identifying PPIs between hCoV-2 and its target human proteins. Overlapping genes were identified between the protein-coding genes of the target and COVID-19-infected patient's mRNA expression data. Pathway and Gene Ontology (GO) term analyses, the construction of PPI networks, and the detection of hub gene modules were performed. Structure-based virtual screening with antiviral compounds was performed to identify potential hits against target gene-encoded protein. Results: This study predicted 19,051 unique target human proteins that interact with hCoV-2, and compared to the microarray dataset, 1,120 target and infected group differentially expressed genes (TIG-DEGs) were identified. The significant pathway and GO enrichment analyses revealed the involvement of these genes in several biological processes and molecular functions. PPI network analysis identified a significant hub gene with maximum neighboring partners. Virtual screening analysis identified three potential antiviral compounds against the target gene-encoded protein. Conclusion: This study provides potential targets for host-targeting drug development against SARS-CoV-2 infection, and further experimental validation of the target protein is required for pharmaceutical intervention.
Collapse
Affiliation(s)
- Alvea Tasneem
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Armiya Sultan
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Hridoy R. Bairagya
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Hassan Hussain Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | | | - Abdulkarim S. Binshaya
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Bader S. Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Alaa Abdulaziz Eisa
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | | | - Mohammad Raghibul Hasan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Kapil Dev
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
54
|
Dikhit MR, Sen A. Elucidation of conserved multi-epitope vaccine against Leishmania donovani using reverse vaccinology. J Biomol Struct Dyn 2024; 42:1293-1306. [PMID: 37054523 DOI: 10.1080/07391102.2023.2201630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/29/2023] [Indexed: 04/15/2023]
Abstract
Visceral leishmaniasis (VL) is a tropical disease that causes severe public health problems in humans when untreated. As no licensed vaccine exists against VL, we aimed to formulate a potential MHC-restricted chimeric vaccine construct against this dreadful parasitic disease. Amastin-like protein derived from L. donovani is considered to be stable, immunogenic and non-allergic. A comprehensive established framework was used to explore the set of immunogenic epitopes with estimated population coverage of 96.08% worldwide. The rigorous assessment revealed 6 promiscuous T-epitopes which can plausibly be presented by more than 66 diverse HLA alleles. Further docking and simulation study of peptide receptor complexes identified a strong and stable binding interaction with better structural compactness. The predicted epitopes were combined with appropriate linkers and adjuvant molecules and their translation efficiency was evaluated in pET28+(a), an bacterial expression vector using in-silico cloning. Molecular docking followed by MD simulation study revealed a stable interaction between chimeric vaccine construct with TLRs. Immune simulation of the chimeric vaccine constructs showed an elevated Th1 immune response against both B and T epitopes. With this, the detailed computational analysis suggested that the chimeric vaccine construct can evoke a robust immune response against Leishmania donovani infection. Future studies are required to validate the role of amastin as a promising vaccine target.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Manas Ranjan Dikhit
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Abhik Sen
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| |
Collapse
|
55
|
Thapa R, Roy A, Nayek K, Basu A. Identification of a Novel Homozygous Missense Mutation in the CLDN16 Gene to Decipher the Ambiguous Clinical Presentation Associated with Autosomal Dominant Hypocalcaemia and Familial Hypomagnesemia with Hypercalciuria and Nephrocalcinosis in an Indian Family. Calcif Tissue Int 2024; 114:110-118. [PMID: 38078932 DOI: 10.1007/s00223-023-01142-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/14/2023] [Indexed: 01/23/2024]
Abstract
Familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHNNC) is a rare autosomal recessive renal tubulopathy disorder characterized by excessive urinary loss of calcium and magnesium, polyuria, polydipsia, bilateral nephrocalcinosis, progressive chronic kidney disease, and renal failure. Also, sometimes amelogenesis imperfecta and severe ocular abnormalities are involved. The CLDN-16 and CLDN-19 genes encode the tight junction proteins claudin-16 and claudin-19, respectively, in the thick ascending loop of Henle in the kidney, epithelial cells of the retina, dental enamel, etc. Loss of function of the CLDN-16 and/or CLDN-19 genes leads to FHHNC. We present a case of FHHNC type 1, which was first confused with autosomal dominant hypocalcaemia (ADH) due to the presence of a very low serum parathyroid hormone (PTH) concentration and other similar clinical features before the genetic investigations. After the exome sequencing, FHHNC type 1 was confirmed by uncovering a novel homozygous missense mutation in the CLDN-16 gene (Exon 2, c.374 T > C) which causes, altered protein structure with F55S. Associated clinical, biochemical, and imaging findings also corroborate final diagnosis. Our findings expand the spectrum of the CLDN-16 mutation, which will further help in the genetic diagnosis and management of FHNNC.
Collapse
Affiliation(s)
- Rupesh Thapa
- The University of Burdwan, Burdwan, WB, India
- National Institute of Biomedical Genomics, Kalyani, WB, India
| | - Amaresh Roy
- Department of Paediatric Medicine, Burdwan Medical College, and Hospital, Burdwan, WB, India
| | - Kaustav Nayek
- Department of Paediatric Medicine, Burdwan Medical College, and Hospital, Burdwan, WB, India.
| | - Anupam Basu
- The University of Burdwan, Burdwan, WB, India.
- National Institute of Biomedical Genomics, Kalyani, WB, India.
| |
Collapse
|
56
|
Bahoussi AN, Shah PT, Liu Y, Guo YY, Bu H, Wu C, Xing L. Evolutionary History and Genetic Variation of Zika Virus: Connection Between Thailand Zika Viruses and Global Outbreaks Strains. Vector Borne Zoonotic Dis 2024; 24:122-128. [PMID: 37890113 DOI: 10.1089/vbz.2023.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023] Open
Abstract
Background: Zika virus (ZIKV) has significant potential to cause future outbreaks due to insufficient countermeasures. The evolution of ZIKV in Southeast Asian countries remains poorly understood. Materials and Methods: The phylogenetic, phylogeographic network, and recombination analyses of 366 ZIKV complete genome sequences identified between 1947 and 2021 were performed and the amino acid variation landscape was determined to reveal the evolutionary characteristics. Results: ZIKV falls into two major genogroups: GI and GII, segregated into further subgenogroups (GI-1 to GI-3) and (GII-1 to GII-3), respectively. Importantly, Thailand strains cluster with Southeast Asian outbreak strains (Singapore 2016, the Philippines 2012, Cambodia 2010) into GII-2 and form a lineage independent of French Polynesia and the Americas large outbreak strains. Thailand ZIKV strains shared their ancestral route to the strains from French Polynesia, which further connects to Brazil ZIKV through a short mutational branch. Both recombination and specific mutations may contribute to the emergence of new virus lineage in Thailand. Conclusion: This report provides insights into the evolutionary characteristics of ZIKV in Southeast Asia, which may be helpful for epidemiological investigation, vaccine development, and surveillance of the virus.
Collapse
Affiliation(s)
| | - Pir Tariq Shah
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Yue Liu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Yan-Yan Guo
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Hongli Bu
- Department of Laboratory Medicine, The Fourth People's Hospital of Taiyuan, Taiyuan, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
| |
Collapse
|
57
|
Kavousi S, Dalili M, Rabbani B, Behmanesh M, Noruzinia M, Mahdieh N. A Mutational Hotspot in The LAMP2 Gene: Unravelling Intrafamilial Phenotypic Variation and Global Distribution of The c.877C>T Variant: A Descriptive Study. CELL JOURNAL 2024; 26:39-50. [PMID: 38351728 PMCID: PMC10864773 DOI: 10.22074/cellj.2023.2007469.1372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/14/2023] [Accepted: 11/08/2023] [Indexed: 02/18/2024]
Abstract
OBJECTIVE Danon disease is defined by a clinical trio of cardiomyopathy, skeletal myopathy, and cognitive impairment. It results from the lysosomal-associated membrane protein-2 (LAMP2) gene variants. The aim of study is determination of genotype and phenotype of a newly diagnosed Iranian family with a unique phenotype due to a pathogenic variant of the LAMP2 gene along with a phenotypic comparison of all reported patients. MATERIALS AND METHODS In this descriptive study, we evaluated the demographic data, clinical features, management procedures, as well as genetic analysis of both patients in this newly diagnosed family. Whole genome sequencing (WGS) and in silico structural and functional predictions were applied. A comprehensive search of the c.877C>T variant in LAMP2 was conducted using the PubMed, Google Scholar, VarSome, ClinVar, Human Gene Mutation Database (HGMD), and Franklin databases to identify any genotype-phenotype correlations. RESULTS Nine patients were carriers of the c.877C>T variant. All patients were male, and displayed variable degrees of left ventricular hypertrophy (LVH) that ranged from mild to severe. All patients exhibited typical cardiac conduction abnormalities consistent with Danon disease. Four underwent heart transplants and survived. Skeletal muscle involvement and cognitive impairment were observed in four patients each. The mean age of onset was 14 years. The proband in this study exhibited an earlier onset of cardiac symptoms. CONCLUSION Genetic analysis is the preferred diagnosis approach for Danon disease and can assist families in managing affected patients, identify carriers, and assist with future family planning. This study highlights the intrafamilial phenotypic variability of Danon disease. It is possible that variants of this gene may be frequent in Iran.
Collapse
Affiliation(s)
- Saeideh Kavousi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Dalili
- Rajaie Cardiovascular Medical and Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Bahareh Rabbani
- Growth and Development Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehrdad Noruzinia
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Nejat Mahdieh
- Cardiogenetic Research Centre, Rajaie Cardiovascular Medical and Research Centre, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
58
|
Wang CW, Weaver SD, Boonpattrawong N, Schuster-Little N, Patankar M, Whelan RJ. A Revised Molecular Model of Ovarian Cancer Biomarker CA125 (MUC16) Enabled by Long-read Sequencing. CANCER RESEARCH COMMUNICATIONS 2024; 4:253-263. [PMID: 38197671 PMCID: PMC10829539 DOI: 10.1158/2767-9764.crc-23-0327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/01/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
The biomarker CA125, a peptide epitope located in several tandem repeats of the mucin MUC16, is the gold standard for monitoring regression and recurrence of high-grade serous ovarian cancer in response to therapy. However, the CA125 epitope along with several structural features of the MUC16 molecule are ill defined. One central aspect still unresolved is the number of tandem repeats in MUC16 and how many of these repeats contain the CA125 epitope. Studies from the early 2000s assembled short DNA reads to estimate that MUC16 contained 63 repeats.Here, we conduct Nanopore long-read sequencing of MUC16 transcripts from three primary ovarian tumors and established cell lines (OVCAR3, OVCAR5, and Kuramochi) for a more exhaustive and accurate estimation and sequencing of the MUC16 tandem repeats.The consensus sequence derived from these six sources was confirmed by proteomics validation and agrees with recent additions to the NCBI database. We propose a model of MUC16 containing 19-not 63-tandem repeats. In addition, we predict the structure of the tandem repeat domain using the deep learning algorithm, AlphaFold.The predicted structure displays an SEA domain and unstructured linker region rich in proline, serine, and threonine residues in all 19 tandem repeats. These studies now pave the way for a detailed characterization of the CA125 epitope. Sequencing and modeling of the MUC16 tandem repeats along with their glycoproteomic characterization, currently underway in our laboratories, will help identify novel epitopes in the MUC16 molecule that improve on the sensitivity and clinical utility of the current CA125 assay. SIGNIFICANCE Despite its crucial role in clinical management of ovarian cancer, the exact molecular sequence and structure of the biomarker, CA125, are not defined. Here, we combine long-read sequencing, mass spectrometry, and in silico modeling to provide the foundational dataset for a more complete characterization of the CA125 epitope.
Collapse
Affiliation(s)
- Chien-Wei Wang
- Department of Chemistry, University of Kansas, Lawrence, Kansas
| | - Simon D. Weaver
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, Indiana
| | - Nicha Boonpattrawong
- Department of Obstetrics and Gynecology, University of Wisconsin–Madison, Madison, Wisconsin
| | | | - Manish Patankar
- Department of Obstetrics and Gynecology, University of Wisconsin–Madison, Madison, Wisconsin
| | | |
Collapse
|
59
|
van Zyl EM, Coburn JM. Functionalization of Bacterial Cellulose with the Antimicrobial Peptide KR-12 via Chimerical Cellulose-Binding Peptides. Int J Mol Sci 2024; 25:1462. [PMID: 38338739 PMCID: PMC10855235 DOI: 10.3390/ijms25031462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Bacterial-derived cellulose (BC) has been studied as a promising material for biomedical applications, including wound care, due to its biocompatibility, water-holding capacity, liquid/gas permeability, and handleability properties. Although BC has been studied as a dressing material for cutaneous wounds, to date, BC inherently lacks antibacterial properties. The current research utilizes bifunctional chimeric peptides containing carbohydrate binding peptides (CBP; either a short version or a long version) and an antimicrobial peptide (AMP), KR-12. The secondary structure of the chimeric peptides was evaluated and confirmed that the α-helix structure of KR-12 was retained for both chimeric peptides evaluated (Long-CBP-KR12 and Short-CBP-KR12). Chimeric peptides and their individual components were assessed for cytotoxicity, where only higher concentrations of Short-CBP and longer timepoints of Short-CBP-KR12 exposure exhibited negative effects on metabolic activity, which was attributed to solubility issues. All KR-12-containing peptides exhibited antibacterial activity in solution against Escherichia coli (E. coli) and Pseudomonas aeruginosa (P. aeruginosa). The lipopolysaccharide (LPS) binding capability of the peptides was evaluated and the Short-CBP-KR12 peptide exhibited enhanced LPS-binding capabilities compared to KR-12 alone. Both chimeric peptides were able to bind to BC and were observed to be retained on the surface over a 7-day period. All functionalized materials exhibited no adverse effects on the metabolic activity of both normal human dermal fibroblasts (NHDFs) and human epidermal keratinocyte (HaCaT) epithelial cells. Additionally, the BC tethered chimeric peptides exhibited antibacterial activity against E. coli. Overall, this research outlines the design and evaluation of chimeric CBP-KR12 peptides for developing antimicrobial BC membranes with potential applications in wound care.
Collapse
Affiliation(s)
| | - Jeannine M. Coburn
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| |
Collapse
|
60
|
Tian C, Zhao N, Yang L, Lin F, Cai R, Zhang Y, Peng J, Guo G. The antibacterial activity and mechanism of a novel peptide MR-22 against multidrug-resistant Escherichia coli. Front Cell Infect Microbiol 2024; 14:1334378. [PMID: 38328670 PMCID: PMC10847306 DOI: 10.3389/fcimb.2024.1334378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
Introduction Bacterial infections have become serious threats to human health, and the excessive use of antibiotics has led to the emergence of multidrug-resistant (MDR) bacteria. E. coli is a human bacterial pathogen, which can cause severe infectious. Antimicrobial peptides are considered the most promising alternative to traditional antibiotics. Materials and methods The minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and hemolytic activity were determined by the microdilution method. The antimicrobial kinetics of MR-22 against E. coli were studied by growth curves and time-killing curves. The cytotoxicity of MR-22 was detected by the CCK-8 assay. The antimicrobial activity of MR-22 in salt, serum, heat and trypsin was determined by the microdilution method. The antimicrobial mechanism of MR-22 against drug-resistant E. coli was studied by Scanning Electron Microscope, laser confocal microscopy, and Flow Cytometry. The in vivo antibacterial activity of MR-22 was evaluated by the mice model of peritonitis. Results and discussion In this study, MR-22 is a new antimicrobial peptide with good activity that has demonstrated against MDR E. coli. The antimicrobial activity of MR-22 exhibited stability under conditions of high temperature, 10% FBS, and Ca2+. However, a decline of the activity was observed in the presence of Na+, serum, and trypsin. MR-22 had no significant cytotoxicity or hemolysis in vitro. SEM and fluorescent images revealed that MR-22 could disrupt the integrity of cell membrane. DCFH-DA indicated that MR-22 increased the content of reactive oxygen species, while it decreased the content of intracellular ATP. In mice model of peritonitis, MR-22 exhibited potent antibacterial activity in vivo. These results indicated that MR-22 is a potential drug candidate against drug-resistant E. coli.
Collapse
Affiliation(s)
- Chunren Tian
- School of Basic Medical Sciences, The Key and Characteristic Laboratory of Modern Pathogen Biology, Guizhou Medical University, Guiyang, China
- Clinical Laboratory, Guiyang Hospital of Guizhou Aviation Industry Group, Guiyang, China
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
| | - Na Zhao
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
- Translational Medicine Research Center, Guizhou Medical University, Guiyang, China
| | - Longbing Yang
- School of Basic Medical Sciences, The Key and Characteristic Laboratory of Modern Pathogen Biology, Guizhou Medical University, Guiyang, China
| | - Fei Lin
- School of Basic Medical Sciences, The Key and Characteristic Laboratory of Modern Pathogen Biology, Guizhou Medical University, Guiyang, China
| | - Ruxia Cai
- School of Basic Medical Sciences, The Key and Characteristic Laboratory of Modern Pathogen Biology, Guizhou Medical University, Guiyang, China
| | - Yong Zhang
- School of Basic Medical Sciences, The Key and Characteristic Laboratory of Modern Pathogen Biology, Guizhou Medical University, Guiyang, China
| | - Jian Peng
- School of Basic Medical Sciences, The Key and Characteristic Laboratory of Modern Pathogen Biology, Guizhou Medical University, Guiyang, China
| | - Guo Guo
- School of Basic Medical Sciences, The Key and Characteristic Laboratory of Modern Pathogen Biology, Guizhou Medical University, Guiyang, China
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
- Translational Medicine Research Center, Guizhou Medical University, Guiyang, China
| |
Collapse
|
61
|
Khatua S, Roy A, Sen P, Ray S. Elucidation of the structural dynamics of mutations in PHB2 protein associated with growth suppression and cancer progression. Gene 2024; 890:147820. [PMID: 37739195 DOI: 10.1016/j.gene.2023.147820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/03/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Prohibitin is a multifunctional protein that plays an important role in numerous cellular processes. Membrane-associated mitochondrial prohibitin complex is made up of two subunits, PHB1 and PHB2 which are ubiquitously expressed and analogous to each other. High levels of prohibitin expression have consequently been found in esophageal cancer, endometrial adenocarcinoma, gastric cancer, hepatocellular carcinoma, breast cancer and bladder cancer. The aim of this study is to analyse two-point mutation PHB2_MT1(I → A) and PHB2_MT2(I → P), their effect on PHB2 protein and its effect on formation of mitochondrial complex. It is a residual level study, based on current experimental validation. To establish the effects of the two-point mutations, computational approaches such as molecular modelling, molecular docking, normal mode simulation, molecular dynamics simulations and MM/GBSA were used. An analysis of the energy dynamics of both unbound and complex proteins was conducted to elucidate how mutations impact the energy distribution of PHB2. Our study confirmed that the two mutations decreased the overall stability of PHB2. This was evidenced by heightened atomic fluctuations within the mutated region, accompanied by elevated deviations observed in RMSD and Rg values. Furthermore, these mutations were correlated with a decline in the organization of secondary structural elements. The mutations in PHB2_MT1 and PHB2_MT2 resulted in formation a less stable prohibitin complex. Thus, PHB1 and PHB2 may act as molecular target or novel biomarkers for therapeutic intervention in numerous forms of malignancies.
Collapse
Affiliation(s)
- Susmita Khatua
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Alankar Roy
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Pritha Sen
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India.
| |
Collapse
|
62
|
Azad MTA, Sugi T, Qulsum U, Kato K. Detection of Developmental Asexual Stage-Specific RNA Editing Events in Plasmodium falciparum 3D7 Malaria Parasite. Microorganisms 2024; 12:137. [PMID: 38257964 PMCID: PMC10819399 DOI: 10.3390/microorganisms12010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Transcriptional variation has been studied but post-transcriptional modification due to RNA editing has not been investigated in Plasmodium. We investigated developmental stage-specific RNA editing in selected genes in Plasmodium falciparum 3D7. We detected extensive amination- and deamination-type RNA editing at 8, 16, 24, 32, 40, and 46 h in tightly synchronized Plasmodium. Most of the editing events were observed in 8 and 16 h ring-stage parasites. Extensive A-to-G deamination-type editing was detected more during the 16 h ring stage (25%) than the 8 h ring stage (20%). Extensive U-to-C amination-type editing was detected more during the 16 h ring stage (31%) than the 8 h ring stage (22%). In 28S, rRNA editing converted the loop structure to the stem structure. The hemoglobin binding activity of PF3D7_0216900 was also altered due to RNA editing. Among the expressed 28S rRNA genes, PF3D7_0532000 and PF3D7_0726000 expression was higher. Increased amounts of the transcripts of these two genes were found, particularly PF3D7_0726000 in the ring stage and PF3D7_0532000 in the trophozoite and schizont stages. Adenosine deaminase (ADA) expression did not correlate with the editing level. This first experimental report of RNA editing will help to identify the editing machinery that might be useful for antimalarial drug discovery and malaria control.
Collapse
Affiliation(s)
- Md Thoufic Anam Azad
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Tatsuki Sugi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Nishi10-Kita 20, Sapporo 001-0020, Japan
| | - Umme Qulsum
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Kentaro Kato
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| |
Collapse
|
63
|
Roy BG, Choi J, Fuchs MF. Predictive Modeling of Proteins Encoded by a Plant Virus Sheds a New Light on Their Structure and Inherent Multifunctionality. Biomolecules 2024; 14:62. [PMID: 38254661 PMCID: PMC10813169 DOI: 10.3390/biom14010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Plant virus genomes encode proteins that are involved in replication, encapsidation, cell-to-cell, and long-distance movement, avoidance of host detection, counter-defense, and transmission from host to host, among other functions. Even though the multifunctionality of plant viral proteins is well documented, contemporary functional repertoires of individual proteins are incomplete. However, these can be enhanced by modeling tools. Here, predictive modeling of proteins encoded by the two genomic RNAs, i.e., RNA1 and RNA2, of grapevine fanleaf virus (GFLV) and their satellite RNAs by a suite of protein prediction software confirmed not only previously validated functions (suppressor of RNA silencing [VSR], viral genome-linked protein [VPg], protease [Pro], symptom determinant [Sd], homing protein [HP], movement protein [MP], coat protein [CP], and transmission determinant [Td]) and previously identified putative functions (helicase [Hel] and RNA-dependent RNA polymerase [Pol]), but also predicted novel functions with varying levels of confidence. These include a T3/T7-like RNA polymerase domain for protein 1AVSR, a short-chain reductase for protein 1BHel/VSR, a parathyroid hormone family domain for protein 1EPol/Sd, overlapping domains of unknown function and an ABC transporter domain for protein 2BMP, and DNA topoisomerase domains, transcription factor FBXO25 domain, or DNA Pol subunit cdc27 domain for the satellite RNA protein. Structural predictions for proteins 2AHP/Sd, 2BMP, and 3A? had low confidence, while predictions for proteins 1AVSR, 1BHel*/VSR, 1CVPg, 1DPro, 1EPol*/Sd, and 2CCP/Td retained higher confidence in at least one prediction. This research provided new insights into the structure and functions of GFLV proteins and their satellite protein. Future work is needed to validate these findings.
Collapse
Affiliation(s)
- Brandon G. Roy
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 15 Castle Creek Drive, Geneva, NY 14456, USA; (J.C.); (M.F.F.)
| | | | | |
Collapse
|
64
|
Wang H, Zhang R, Hu J, Fu R, Li J. In vitro and in silico analyses reveal the interaction between LysM receptor-like kinase3 of Solanum tuberosum and the carbohydrate elicitor Riclin octaose. Biotechnol J 2024; 19:e2300385. [PMID: 37903287 DOI: 10.1002/biot.202300385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 11/01/2023]
Abstract
As a carbohydrate elicitor, Riclin octaose (Rioc) activates the pattern-triggered immunity of Solanum tuberosum L., while how the plant perceives Rioc is unknown. Here, a pattern recognition receptor StLYK3 (LysM receptor-like kinase3) whose transcription level was significantly up-regulated after Rioc elicitation was investigated in vitro and in silico. The nucleotide that encoded the ectodomain of StLYK3 (StLYK3-ECD) was heterologously expressed in the Pichia pastoris strain GS115. The purified StLYK3-ECD had the molecular weight of 25.08 kDa and pI of 5.69. Afterwards interaction between StLYK3-ECD and Rioc was analyzed by isothermal titration calorimetry. The molar ratio of ligand to receptor, dissociation constant, and enthalpy were 1.28 ± 0.04, 26.7 ± 3.1 μM, and -45.0 ± 1.8 kJ mol-1 , respectively. Besides, molecular dynamics results indicated that StLYK3-ECD contained three carbohydrate-binding motifs and the first two motifs probably contributed to the interaction with Rioc via hydrogen bond and van de Waals' forces. Amino acids containing hydroxyl, amidic, and sulfhydryl groups took the main portion in the docking site. Moreover, replacing the 92nd threonyl (T) of StLYK3-ECD with valyl (V) resulted in the alteration of the preferred docking site. The dissociation constant drastically increased to 841.6 ± 232.4 μM. In conclusion, StLYK3 was a potential receptor of Rioc.
Collapse
Affiliation(s)
- Hongyang Wang
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Ruixin Zhang
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Junpeng Hu
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Renjie Fu
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Jing Li
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
- Center for Molecular Metabolism, Nanjing University of Science and Technology, Nanjing, China
| |
Collapse
|
65
|
Arthur MN, Bebla K, Broni E, Ashley C, Velazquez M, Hua X, Radhakrishnan R, Kwofie SK, Miller WA. Design of Inhibitors That Target the Menin-Mixed-Lineage Leukemia Interaction. COMPUTATION (BASEL, SWITZERLAND) 2024; 12:3. [PMID: 38938622 PMCID: PMC11209892 DOI: 10.3390/computation12010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
The prognosis of mixed-lineage leukemia (MLL) has remained a significant health concern, especially for infants. The minimal treatments available for this aggressive type of leukemia has been an ongoing problem. Chromosomal translocations of the KMT2A gene are known as MLL, which expresses MLL fusion proteins. A protein called menin is an important oncogenic cofactor for these MLL fusion proteins, thus providing a new avenue for treatments against this subset of acute leukemias. In this study, we report results using the structure-based drug design (SBDD) approach to discover potential novel MLL-mediated leukemia inhibitors from natural products against menin. The three-dimensional (3D) protein model was derived from Protein Databank (Protein ID: 4GQ4), and EasyModeller 4.0 and I-TASSER were used to fix missing residues during rebuilding. Out of the ten protein models generated (five from EasyModeller and I-TASSER each), one model was selected. The selected model demonstrated the most reasonable quality and had 75.5% of residues in the most favored regions, 18.3% of residues in additionally allowed regions, 3.3% of residues in generously allowed regions, and 2.9% of residues in disallowed regions. A ligand library containing 25,131 ligands from a Chinese database was virtually screened using AutoDock Vina, in addition to three known menin inhibitors. The top 10 compounds including ZINC000103526876, ZINC000095913861, ZINC000095912705, ZINC000085530497, ZINC000095912718, ZINC000070451048, ZINC000085530488, ZINC000095912706, ZINC000103580868, and ZINC000103584057 had binding energies of -11.0, -10.7, -10.6, -10.2, -10.2, -9.9, -9.9, -9.9, -9.9, and -9.9 kcal/mol, respectively. To confirm the stability of the menin-ligand complexes and the binding mechanisms, molecular dynamics simulations including molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) computations were performed. The amino acid residues that were found to be potentially crucial in ligand binding included Phe243, Met283, Cys246, Tyr281, Ala247, Ser160, Asn287, Asp185, Ser183, Tyr328, Asn249, His186, Leu182, Ile248, and Pro250. MI-2-2 and PubChem CIDs 71777742 and 36294 were shown to possess anti-menin properties; thus, this justifies a need to experimentally determine the activity of the identified compounds. The compounds identified herein were found to have good pharmacological profiles and had negligible toxicity. Additionally, these compounds were predicted as antileukemic, antineoplastic, chemopreventive, and apoptotic agents. The 10 natural compounds can be further explored as potential novel agents for the effective treatment of MLL-mediated leukemia.
Collapse
Affiliation(s)
- Moses N. Arthur
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Biomedical Engineering Department, University of Rochester, Rochester, NY 14627, USA
| | - Kristeen Bebla
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Carolyn Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Miriam Velazquez
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Xianin Hua
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
66
|
Kazemi-Lomedasht F, Taghizadeh-Hesary F, Faal Z, Behdani M. Targeted Delivery of Diphtheria Toxin into VEGFR1/VEGFR2 Overexpressing Cells Induces Anti-angiogenesis Activity. Curr Protein Pept Sci 2024; 25:567-576. [PMID: 39044556 DOI: 10.2174/0113892037292385240222074908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 07/25/2024]
Abstract
BACKGROUND Vascular Endothelial Growth Factor Receptors (VEGFR1 and VEGFR2) are tyrosine kinase receptors expressed on endothelial cells and tumor vessels and play an important role in angiogenesis. In this study, three repeats of VEGFR1 and VEGFR2 binding peptide (VGB3) were genetically fused to the truncated diphtheria toxin (TDT), and its in vitro activity was evaluated. METHODS The recombinant construct (TDT-triVGB3) was expressed in bacteria cells and purified with nickel affinity chromatography. The binding capacity and affinity of TDT-triVGB3 were evaluated using the enzyme-linked immunosorbent assay. The inhibitory activity of TDT-triVGB3 on viability, migration, and tube formation of human endothelial cells was evaluated using MTT, migration, and tube formation assays. RESULTS TDT-triVGB3 selectively detected VEGFR1 and VEGFR2 with high affinity in an enzyme- linked immunosorbent assay and significantly inhibited viability, migration, and tube formation of human endothelial cells. CONCLUSION The developed TDT-triVGB3 is potentially a novel agent for targeting VEGFR1/ VEGFR2 over-expressing cancer cells.
Collapse
Affiliation(s)
- Fatemeh Kazemi-Lomedasht
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Farzad Taghizadeh-Hesary
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Clinical Oncology Department, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Faal
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mahdi Behdani
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
67
|
Santamaria S. Web-Based Resources to Investigate Protease Function. Methods Mol Biol 2024; 2747:1-18. [PMID: 38038927 DOI: 10.1007/978-1-0716-3589-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
In 2001, the release of the first draft of the human genome marked the beginning of the Big Data era for biological sciences. Since then, the complexity of datasets generated by laboratories worldwide has increased exponentially. Public repositories such as the Protein Data Bank, which has exceeded the 200000 entries in 2023, have been instrumental not only to collect, organize, and distill this enormous research output but also to promote further research enterprises. The achievements of artificial intelligence programs such as AlphaFold would not have been possible without the collective efforts of countless researchers who made their work publicly available. Here, I provide a practical, but far from exhaustive, list of resources useful to investigate protease function.
Collapse
Affiliation(s)
- Salvatore Santamaria
- Department of Biochemical Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK.
| |
Collapse
|
68
|
Arend C, Grothaus IL, Waespy M, Ciacchi LC, Dringen R. Modulation of Multidrug Resistance Protein 1-mediated Transport Processes by the Antiviral Drug Ritonavir in Cultured Primary Astrocytes. Neurochem Res 2024; 49:66-84. [PMID: 37603214 PMCID: PMC10776481 DOI: 10.1007/s11064-023-04008-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023]
Abstract
The Multidrug Resistance Protein 1 (Mrp1) is an ATP-dependent efflux transporter and a major facilitator of drug resistance in mammalian cells during cancer and HIV therapy. In brain, Mrp1-mediated GSH export from astrocytes is the first step in the supply of GSH precursors to neurons. To reveal potential mechanisms underlying the drug-induced modulation of Mrp1-mediated transport processes, we investigated the effects of the antiviral drug ritonavir on cultured rat primary astrocytes. Ritonavir strongly stimulated the Mrp1-mediated export of glutathione (GSH) by decreasing the Km value from 200 nmol/mg to 28 nmol/mg. In contrast, ritonavir decreased the export of the other Mrp1 substrates glutathione disulfide (GSSG) and bimane-glutathione. To give explanation for these apparently contradictory observations, we performed in silico docking analysis and molecular dynamics simulations using a homology model of rat Mrp1 to predict the binding modes of ritonavir, GSH and GSSG to Mrp1. The results suggest that ritonavir binds to the hydrophilic part of the bipartite binding site of Mrp1 and thereby differently affects the binding and transport of the Mrp1 substrates. These new insights into the modulation of Mrp1-mediated export processes by ritonavir provide a new model to better understand GSH-dependent detoxification processes in brain cells.
Collapse
Affiliation(s)
- Christian Arend
- Centre for Biomolecular Interactions Bremen, Faculty 2 (Biology/Chemistry), University of Bremen, P.O. Box 330440, 28359, Bremen, Germany.
- Centre for Environmental Research and Sustainable Technology, University of Bremen, Bremen, Germany.
| | - Isabell L Grothaus
- Centre for Environmental Research and Sustainable Technology, University of Bremen, Bremen, Germany
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, MAPEX Center for Materials and Processes, University of Bremen, Am Fallturm 1, 28359, Bremen, Germany
| | - Mario Waespy
- Centre for Biomolecular Interactions Bremen, Faculty 2 (Biology/Chemistry), University of Bremen, P.O. Box 330440, 28359, Bremen, Germany
| | - Lucio Colombi Ciacchi
- Centre for Environmental Research and Sustainable Technology, University of Bremen, Bremen, Germany
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, MAPEX Center for Materials and Processes, University of Bremen, Am Fallturm 1, 28359, Bremen, Germany
| | - Ralf Dringen
- Centre for Biomolecular Interactions Bremen, Faculty 2 (Biology/Chemistry), University of Bremen, P.O. Box 330440, 28359, Bremen, Germany
- Centre for Environmental Research and Sustainable Technology, University of Bremen, Bremen, Germany
| |
Collapse
|
69
|
Patel KM, Seed KD. Sporadic phage defense in epidemic Vibrio cholerae mediated by the toxin-antitoxin system DarTG is countered by a phage-encoded antitoxin mimic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571748. [PMID: 38168179 PMCID: PMC10760071 DOI: 10.1101/2023.12.14.571748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Bacteria and their viral predators (phages) are constantly evolving to subvert one another. Many bacterial immune systems that inhibit phages are encoded on mobile genetic elements that can be horizontally transmitted to diverse bacteria. Despite the pervasive appearance of immune systems in bacteria, it is not often known if these immune systems function against phages that the host encounters in nature. Additionally, there are limited examples demonstrating how these phages counter-adapt to such immune systems. Here, we identify clinical isolates of the global pathogen Vibrio cholerae harboring a novel genetic element encoding the bacterial immune system DarTG and reveal the immune system's impact on the co-circulating lytic phage ICP1. We show that DarTG inhibits ICP1 genome replication, thus preventing ICP1 plaquing. We further characterize the conflict between DarTG-mediated defense and ICP1 by identifying an ICP1-encoded protein that counters DarTG and allows ICP1 progeny production. Finally, we identify this protein as a functional antitoxin that abrogates the toxin DarT likely through direct interactions. Following the detection of the DarTG system in clinical V. cholerae isolates, we observed a rise in ICP1 isolates with the functional antitoxin. These data highlight the use of surveillance of V. cholerae and its lytic phages to understand the co-evolutionary arms race between bacteria and their phages in nature.
Collapse
Affiliation(s)
- Kishen M Patel
- Infectious Diseases and Immunity Graduate Group, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| |
Collapse
|
70
|
Song P, Zhao L, Zhu L, Sha G, Dong W. BsR1, a broad-spectrum antibacterial peptide with potential for plant protection. Microbiol Spectr 2023; 11:e0257823. [PMID: 37948344 PMCID: PMC10714738 DOI: 10.1128/spectrum.02578-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE This study addresses the critical need for new antibacterial drugs in the face of bacterial multidrug resistance resulting from antibiotic overuse. It highlights the significance of antimicrobial peptides as essential components of innate immunity in animals and plants, which have been proven effective against multidrug-resistant bacteria and are difficult to develop resistance against. This study successfully synthesizes a broad-spectrum antibacterial peptide, BsR1, with strong inhibitory activities against various Gram-positive and Gram-negative bacteria. BsR1 demonstrates favorable stability and a mode of action that damages bacterial cell membranes, leading to cell death. It also exhibits biological safety and shows potential in enhancing disease resistance in rice. This research offers a novel approach and potential medication for antibacterial drug development, presenting a valuable tool in combating pathogenic microorganisms, particularly in plants.
Collapse
Affiliation(s)
- Pei Song
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Li Zhao
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Li Zhu
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Gan Sha
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Wubei Dong
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
71
|
Abd El-Aziz NM, Moharam ME, El-Gamal NN, Khalil BE. Enhancement of novel Endo-polygalacturonase expression in Rhodotorula mucilaginosa PY18: insights from mutagenesis and molecular docking. Microb Cell Fact 2023; 22:252. [PMID: 38066588 PMCID: PMC10709964 DOI: 10.1186/s12934-023-02253-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Pectinase is a particular type of enzyme that can break down pectin compounds and is extensively utilised in the agricultural field. In this study, twenty yeast isolates were isolated and assayed for pectinase activity. Molecular identification by PCR amplification and sequencing of internal transcribed spacer (ITS) regions of isolate no. 18 had the highest pectinase activity of 46.35 U/mg, was identified as Rhodotorula mucilaginosa PY18, and was submitted under accession no. (OM275426) in NCBI. Rhodotorula mucilaginosa PY18 was further enhanced through sequential mutagenesis, resulting in a mutant designated as Rhodotorula mucilaginosa E54 with a specific activity of 114.2 U/mg. Using Response Surface Methodology (RSM), the best culture conditions for the pectinase-producing yeast mutant Rhodotorula mucilaginosa E54 were pH 5, 72-h incubation, 2.5% xylose, and 2.5% malt extract, with a pectinase-specific activity of 156.55 U/mg. Then, the obtained sequences of the endo-polygalacturonase PGI gene from Rhodotorula mucilaginosa PY18 and mutant Rhodotorula mucilaginosa E54 were isolated for the first time, sequenced, and submitted to NCBI accession numbers OQ283005 and OQ283006, respectively. The modelled 3D structure of the endo-PGI enzyme (485 residues) was validated using Ramachandran's plot, which showed 87.71, 85.56, and 91.57% in the most favourable region for template Rhodotorula mucilaginosa KR, strain Rhodotorula mucilaginosa PY18, and mutant Rhodotorula mucilaginosa E54, respectively. In molecular docking studies, the results of template Rhodotorula mucilaginosa KR endo-PG1 showed an interaction with an affinity score of - 6.0, - 5.9, and - 5.6 kcal/mol for active sites 1, 2, and 3, respectively. Rhodotorula mucilaginosa PY18 endo-PG1 showed an interaction affinity with a score of - 5.8, - 6.0, and - 5.0 kcal/mol for active sites 1, 2, and 3, respectively. Mutant Rhodotorula mucilaginosa E54 endo-PG1 showed an interaction affinity of - 5.6, - 5.5, - 5.5 and - 5.4 kcal/mol for active sites 1, 2, and 3, respectively. The endo-PGI genes of both the yeast strain Rhodotorula mucilaginosa PY18 and mutant Rhodotorula mucilaginosa E54 were successfully cloned and expressed in E. coli DH5α, showing significantly higher endo-PG1 activity, which recorded 94.57 and 153.10 U/mg for recombinant Rhodotorula mucilaginosa pGEM-PGI-PY18 and recombinant mutant Rhotorula pGEM-PGI-E54, respectively.
Collapse
Affiliation(s)
- Nagwa M Abd El-Aziz
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St, Dokki, Cairo, 12622, Egypt.
| | - Maysa E Moharam
- Microbial Chemistry Department, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St, Dokki, Cairo, 12622, Egypt
| | - Nora N El-Gamal
- Microbial Chemistry Department, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St, Dokki, Cairo, 12622, Egypt
| | - Bigad E Khalil
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St, Dokki, Cairo, 12622, Egypt
| |
Collapse
|
72
|
Nguyen M, Maria AG, Faucz FR, Trivellin G, Stratakis CA, Tatsi C. FAF1 Gene Involvement in Pituitary Corticotroph Tumors. Horm Metab Res 2023. [PMID: 38065537 DOI: 10.1055/a-2192-1761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Cushing's disease (CD) is caused by rare pituitary corticotroph tumors that lead to corticotropin (ACTH) excess. Variants in FAF1, a pro-apoptotic protein involved in FAS-induced cell death, have been implicated in malignant disorders but the involvement of FAF1 in pituitary tumors has not been studied. Genetic data from patients with CD were reviewed for variants in FAF1 gene. Knockout mice (KO) were followed to assess the development of any pituitary disorder or cortisol excess. AtT-20 cells were used to study the effects of the variants of interest on ACTH secretion and cell proliferation. Three variants of interest were identified in 5 unique patients, two of which had rare allele frequency in genomic databases and were predicted to be likely pathogenic. KO mice were followed over time and no difference in their length/weight was noted. Additionally, KO mice did not develop any pituitary lesions and retained similar corticosterone secretion with wild type. AtT-20 cells transfected with FAF1 variants of interest or WT expression plasmids showed no significant difference in cell death or Pomc gene expression. However, in silico prediction models suggested significant differences in secondary structures of the produced proteins. In conclusion, we identified two FAF1 variants in patients diagnosed with CD with a potential pathogenic effect on the protein function and structure. Our in vitro and in vivo studies did not reveal an association of FAF1 defects with pituitary tumorigenesis and further studies may be needed to understand any association.
Collapse
Affiliation(s)
- Matthew Nguyen
- Unit on Hypothalamic and Pituitary Disorders, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, United States
| | - Andrea Gutierrez Maria
- Section on Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, United States
| | - Fabio R Faucz
- Molecular Genomics Core (MGC), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, United States
| | - Giampaolo Trivellin
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele - Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano - Milan, Italy
| | - Constantine A Stratakis
- Unit on Hypothalamic and Pituitary Disorders, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, United States
- Human Genetics and Precision Medicine, IMBB, Heraklion, Greece
- Research and Training, ELPEN Pharmaceuticals, Pikermi Attikis, Greece
| | - Christina Tatsi
- Unit on Hypothalamic and Pituitary Disorders, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, United States
| |
Collapse
|
73
|
Hu YT, Hong XZ, Li HM, Yang JK, Shen W, Wang YW, Liu YH. Modifying the amino acids in conformational motion pathway of the α-amylase of Geobacillus stearothermophilus improved its activity and stability. Front Microbiol 2023; 14:1261245. [PMID: 38143856 PMCID: PMC10740195 DOI: 10.3389/fmicb.2023.1261245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/21/2023] [Indexed: 12/26/2023] Open
Abstract
Amino acids along the conformational motion pathway of the enzyme molecule correlated to its flexibility and rigidity. To enhance the enzyme activity and thermal stability, the motion pathway of Geobacillus stearothermophilus α-amylase has been identified and molecularly modified by using the neural relational inference model and deep learning tool. The significant differences in substrate specificity, enzymatic kinetics, optimal temperature, and thermal stability were observed among the mutants with modified amino acids along the pathway. Mutants especially the P44E demonstrated enhanced hydrolytic activity and catalytic efficiency (kcat/KM) than the wild-type enzyme to 95.0% and 93.8% respectively, with the optimum temperature increased to 90°C. This mutation from proline to glutamic acid has increased the number and the radius of the bottleneck of the channels, which might facilitate transporting large starch substrates into the enzyme. The mutation could also optimize the hydrogen bonding network of the catalytic center, and diminish the spatial hindering to the substrate entry and exit from the catalytic center.
Collapse
Affiliation(s)
- Yu-Ting Hu
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Xi-Zhi Hong
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Hui-Min Li
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Jiang-Ke Yang
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Wei Shen
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Ya-Wei Wang
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Yi-Han Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| |
Collapse
|
74
|
Kumaravel A, Selvamani V, Hong SH. Photocatalytic Reduction of Methylene Blue by Surface-Engineered Recombinant Escherichia coli as a Whole-Cell Biocatalyst. Bioengineering (Basel) 2023; 10:1389. [PMID: 38135980 PMCID: PMC10741084 DOI: 10.3390/bioengineering10121389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
A novel Escherichia coli strain, created by engineering its cell surface with a cobalt-binding peptide CP1, was investigated in this study. The recombinant strain, pBAD30-YiaT-CP1, was structurally modeled to determine its cobalt-binding affinity. Furthermore, the effectiveness and specificity of pBAD30-CP1 in adsorbing and extracting cobalt from artificial wastewater polluted with the metal were investigated. The modified cells were subjected to cobalt concentrations (0.25 mM to 1 mM) and pH levels (pH 3, 5, 7, and 9). When exposed to a pH of 7 and a cobalt concentration of 1 mM, the pBAD30-CP1 strain had the best cobalt recovery efficiency, measuring 1468 mol/g DCW (Dry Cell Weight). Furthermore, pBAD30-CP1 had a higher affinity for cobalt than nickel and manganese. Field Emission Scanning Electron Microscopy (FE-SEM), Transmission Electron Microscopy (TEM), and Energy-Dispersive X-ray Spectroscopy (EDS) were used to examine the physiochemical parameters of the recombinant cells after cobalt adsorption. These approaches revealed the presence of cobalt in a bound state on the cell surface in the form of nanoparticles. In addition, the cobalt-binding recombinant strains were used in the photocatalytic reduction of methylene blue, which resulted in a 59.52% drop in the observed percentage. This study shows that modified E. coli strains have the potential for efficient cobalt recovery and application in environmental remediation operations.
Collapse
Affiliation(s)
| | | | - Soon Ho Hong
- Department of Chemical Engineering, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, Republic of Korea; (A.K.); (V.S.)
| |
Collapse
|
75
|
Kumar A, Hooda P, Puri A, Khatter R, S. Al-Dosari M, Sinha N, Parvez MK, Sehgal D. Methotrexate, an anti-inflammatory drug, inhibits Hepatitis E viral replication. J Enzyme Inhib Med Chem 2023; 38:2280500. [PMID: 37975328 PMCID: PMC11003484 DOI: 10.1080/14756366.2023.2280500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Hepatitis E Virus (HEV) is a positively oriented RNA virus having a 7.2 kb genome. HEV consists of three open reading frames (ORF1-3). Of these, ORF1 codes for the enzymes Methyltransferase (Mtase), Papain-like cysteine protease (PCP), RNA helicase, and RNA-dependent RNA polymerase (RdRp). Unavailability of a vaccine or effective drug against HEV and considering the side effects associated with the off-label use of ribavirin (RBV) and pegylated interferons, an alternative approach is required by the modulation of specific enzymes to prevent the infection. HEV helicase is involved in unwinding the double-stranded RNA, RNA processing, transcriptional regulation, and pre-mRNA processing. Therefore, we screened FDA-approved compounds from the ZINC15 database against the modelled 3D structure of HEV helicase and found that methotrexate and compound A (Pubchem ID BTB07890) inhibit the NTPase and dsRNA unwinding activity leading to inhibition of HEV RNA replication. This may be further authenticated by in vivo study.
Collapse
Affiliation(s)
- Akash Kumar
- Department of Life Sciences, Virology lab, Shiv Nadar Institution of Eminence, Greater Noida, India
| | - Preeti Hooda
- Department of Life Sciences, Virology lab, Shiv Nadar Institution of Eminence, Greater Noida, India
| | - Anindita Puri
- Department of Life Sciences, Virology lab, Shiv Nadar Institution of Eminence, Greater Noida, India
| | - Radhika Khatter
- Department of Life Sciences, Virology lab, Shiv Nadar Institution of Eminence, Greater Noida, India
| | - Mohammed S. Al-Dosari
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Neha Sinha
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mohammad K. Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Deepak Sehgal
- Department of Life Sciences, Virology lab, Shiv Nadar Institution of Eminence, Greater Noida, India
| |
Collapse
|
76
|
Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Davies OR, Rommelaere S, Rosas‐Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu K, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins 2023; 91:1571-1599. [PMID: 37493353 PMCID: PMC10792529 DOI: 10.1002/prot.26545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.
Collapse
Affiliation(s)
- Leila T. Alexander
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | - Janani Durairaj
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | - Luciano A. Abriata
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Yusupha Bayo
- Department of BiosciencesUniversity of MilanoMilanItaly
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
| | - Gira Bhabha
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | | | - James Chen
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | - Damian C. Ekiert
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
- Department of MicrobiologyNew York University School of MedicineNew YorkNew YorkUSA
| | - Benedikte S. Erlandsen
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Peter L. Freddolino
- Department of Biological Chemistry, Computational Medicine and BioinformaticsUniversity of MichiganAnn ArborMichiganUSA
| | - Dominic Gilzer
- Department of ChemistryBielefeld UniversityBielefeldGermany
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Securing Antarctica's Environmental FutureMonash UniversityClaytonVictoriaAustralia
- Centre to Impact AMRMonash UniversityClaytonVictoriaAustralia
- ARC Research Hub for Carbon Utilisation and RecyclingMonash UniversityClaytonVictoriaAustralia
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Centre for Electron Microscopy of Membrane ProteinsMonash Institute of Pharmaceutical SciencesParkvilleVictoriaAustralia
| | - Manickam Gurusaran
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Marcus D. Hartmann
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
| | - Charlie J. Hitchman
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Jeremy R. Keown
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Petri Kursula
- Department of BiomedicineUniversity of BergenBergenNorway
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | | | - Bruno Lemaitre
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Andrea Lia
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
- ISPA‐CNR Unit of LecceInstitute of Sciences of Food ProductionLecceItaly
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Maria Logotheti
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
- Present address:
Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - Shuze Lu
- Lanzhou University School of Life SciencesLanzhouChina
| | | | | | - George Minasov
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | | | - Felipe Opazo
- NanoTag Biotechnologies GmbHGöttingenGermany
- Institute of Neuro‐ and Sensory PhysiologyUniversity of Göttingen Medical CenterGöttingenGermany
- Center for Biostructural Imaging of Neurodegeneration (BIN)University of Göttingen Medical CenterGöttingenGermany
| | - George N. Phillips
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Owen R. Davies
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Samuel Rommelaere
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Monica Rosas‐Lemus
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
- Present address:
Department of Molecular Genetics and MicrobiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Pietro Roversi
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Karla Satchell
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | - Nathan Smith
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Kuan‐Lin Wu
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Xian Xia
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Han Xiao
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BioengineeringRice UniversityHoustonTexasUSA
| | - Wenhua Zhang
- Lanzhou University School of Life SciencesLanzhouChina
| | - Z. Hong Zhou
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | | | - Maya Topf
- University Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- Centre for Structural Systems BiologyLeibniz‐Institut für Virologie (LIV)HamburgGermany
| | - John Moult
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Torsten Schwede
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| |
Collapse
|
77
|
Selifanova M, Demianchenko O, Noskova E, Pitikov E, Skvortsov D, Drozd J, Vatolkina N, Apel P, Kolodyazhnaya E, Ezhova MA, Tzetlin AB, Neretina TV, Knorre DA. ORFans in Mitochondrial Genomes of Marine Polychaete Polydora. Genome Biol Evol 2023; 15:evad219. [PMID: 38019573 PMCID: PMC10721130 DOI: 10.1093/gbe/evad219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 11/18/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023] Open
Abstract
Most characterized metazoan mitochondrial genomes are compact and encode a small set of proteins that are essential for oxidative phosphorylation, as well as rRNA and tRNA for their expression. However, in rare cases, invertebrate taxa have additional open reading frames (ORFs) in their mtDNA sequences. Here, we sequenced and analyzed the mitochondrial genome of a polychaete worm, Polydora cf. ciliata, part of whose life cycle takes place in low-oxygen conditions. In the mitogenome, we found three "ORFan" regions (544, 1,060, and 427 bp) that have no resemblance to any standard metazoan mtDNA gene but lack stop codons in one of the reading frames. Similar regions are found in the mitochondrial genomes of three other Polydora species and Bocardiella hamata. All five species share the same gene order in their mitogenomes, which differ from that of other known Spionidae mitogenomes. By analyzing the ORFan sequences, we found that they are under purifying selection pressure and contain conservative regions. The codon adaptation indices (CAIs) of the ORFan genes were in the same range of values as the CAI of conventional protein-coding genes in corresponding mitochondrial genomes. The analysis of the P. cf. ciliata mitochondrial transcriptome showed that ORFan-544, ORFan-427, and a portion of the ORFan-1060 are transcribed. Together, this suggests that ORFan-544 and ORFan-427 encode functional proteins. It is likely that the ORFans originated when the Polydora/Bocardiella species complex separated from the rest of the Spionidae, and this event coincided with massive gene rearrangements in their mitochondrial genomes and tRNA-Met duplication.
Collapse
Affiliation(s)
- Maria Selifanova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg Demianchenko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Elizaveta Noskova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Egor Pitikov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Denis Skvortsov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Jana Drozd
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Nika Vatolkina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Polina Apel
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Kolodyazhnaya
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Margarita A Ezhova
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexander B Tzetlin
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V Neretina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Science, Moscow, Russia
| | - Dmitry A Knorre
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
78
|
Zheng W, Wuyun Q, Freddolino PL, Zhang Y. Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15. Proteins 2023; 91:1684-1703. [PMID: 37650367 PMCID: PMC10840719 DOI: 10.1002/prot.26585] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023]
Abstract
We report the results of the "UM-TBM" and "Zheng" groups in CASP15 for protein monomer and complex structure prediction. These prediction sets were obtained using the D-I-TASSER and DMFold-Multimer algorithms, respectively. For monomer structure prediction, D-I-TASSER introduced four new features during CASP15: (i) a multiple sequence alignment (MSA) generation protocol that combines multi-source MSA searching and a structural modeling-based MSA ranker; (ii) attention-network based spatial restraints; (iii) a multi-domain module containing domain partition and arrangement for domain-level templates and spatial restraints; (iv) an optimized I-TASSER-based folding simulation system for full-length model creation guided by a combination of deep learning restraints, threading alignments, and knowledge-based potentials. For 47 free modeling targets in CASP15, the final models predicted by D-I-TASSER showed average TM-score 19% higher than the standard AlphaFold2 program. We thus showed that traditional Monte Carlo-based folding simulations, when appropriately coupled with deep learning algorithms, can generate models with improved accuracy over end-to-end deep learning methods alone. For protein complex structure prediction, DMFold-Multimer generated models by integrating a new MSA generation algorithm (DeepMSA2) with the end-to-end modeling module from AlphaFold2-Multimer. For the 38 complex targets, DMFold-Multimer generated models with an average TM-score of 0.83 and Interface Contact Score of 0.60, both significantly higher than those of competing complex prediction tools. Our analyses on complexes highlighted the critical role played by MSA generating, ranking, and pairing in protein complex structure prediction. We also discuss future room for improvement in the areas of viral protein modeling and complex model ranking.
Collapse
Affiliation(s)
- Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Qiqige Wuyun
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Peter L Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Computer Science, School of Computing, National University of Singapore, 117417 Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore
| |
Collapse
|
79
|
G P, Rathi B, Santoshi S. Translational and structural vaccinomics approach to design a multi-epitope vaccine against NOL4 autologous antigen of small cell lung cancer. Immunol Res 2023; 71:909-928. [PMID: 37410306 DOI: 10.1007/s12026-023-09404-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/22/2023] [Indexed: 07/07/2023]
Abstract
Small cell lung cancer (SCLC) is one of the most common cancers and it is the sixth common cause for cancer-related deaths. The high plasticity and metastasis have been a major challenge for humanity to treat the disease. Hence, a vaccine for SCLC has become an urgent need of the hour due to public health concern. Implementation of immunoinformatics technique is one of the best way to find a suitable vaccine candidate. Immunoinformatics tools can be used to overcome the limitations and difficulties of traditional vaccinological techniques. Multi-epitope cancer vaccines have become a next-generation technique in vaccinology which can be used to stimulate more potent immune response against a particular antigen by eliminating undesirable molecules. In this study, we used multiple computational and immunoinformatics approach to design a novel multi-epitope vaccine for small cell lung cancer. Nucleolar protein 4 (NOL4) is an autologous cancer-testis antigen overexpressed in SCLC cells. Seventy-five percent humoral immunity have been identified for this particular antigen. In this study, we mapped immunogenic cytotoxic T lymphocyte, helper T lymphocyte, and interferon-gamma epitopes present in NOL4 antigen and designed a multi-epitope-based vaccine using the predicted epitopes. The designed vaccine was antigenic, non-allergenic, and non-toxic with 100% applicability on human population. The chimeric vaccine construct showed stable and significant interaction with endosomal and plasmalemmal toll-like receptors in molecular docking and protein-peptide interaction analysis, thus assuring a strong potent immune response against the vaccine upon administration. Therefore, these preliminary results can be used to carry out further experimental investigations.
Collapse
Affiliation(s)
- Pavithran G
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, India
| | - Bhawna Rathi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India.
| | - Seneha Santoshi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| |
Collapse
|
80
|
Wang J, Chen C, Yao G, Ding J, Wang L, Jiang H. Intelligent Protein Design and Molecular Characterization Techniques: A Comprehensive Review. Molecules 2023; 28:7865. [PMID: 38067593 PMCID: PMC10707872 DOI: 10.3390/molecules28237865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
In recent years, the widespread application of artificial intelligence algorithms in protein structure, function prediction, and de novo protein design has significantly accelerated the process of intelligent protein design and led to many noteworthy achievements. This advancement in protein intelligent design holds great potential to accelerate the development of new drugs, enhance the efficiency of biocatalysts, and even create entirely new biomaterials. Protein characterization is the key to the performance of intelligent protein design. However, there is no consensus on the most suitable characterization method for intelligent protein design tasks. This review describes the methods, characteristics, and representative applications of traditional descriptors, sequence-based and structure-based protein characterization. It discusses their advantages, disadvantages, and scope of application. It is hoped that this could help researchers to better understand the limitations and application scenarios of these methods, and provide valuable references for choosing appropriate protein characterization techniques for related research in the field, so as to better carry out protein research.
Collapse
Affiliation(s)
| | | | | | - Junjie Ding
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (J.W.); (C.C.); (G.Y.)
| | - Liangliang Wang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (J.W.); (C.C.); (G.Y.)
| | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (J.W.); (C.C.); (G.Y.)
| |
Collapse
|
81
|
Akkiraju AG, Badugu A, Das A, Sagurthi SR. Molecular docking-based screening of methicillin-resistant Staphylococcus aureus FEM proteins with FDA-approved drugs. Bioinformation 2023; 19:1035-1042. [PMID: 38046517 PMCID: PMC10692981 DOI: 10.6026/973206300191035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/05/2023] Open
Abstract
Antibiotic resistance stands as one of the most significant public health challenges in recent decades. FEM proteins are responsible for the synthesis of pentaglycine cross-bridge, a primary constituent of bacterial peptidoglycan polymer crosslinking during cell wall biosynthesis. Since they are necessary for bacterial survival and antibiotic resistance, they were considered as significant antibacterial targets. We report herein, the virtual screening and selection of FDA-approved drugs and their potent similar molecules as FEM protein inhibitors and analyzed for inhibiting affinity and their ADMET pharmacokinetic properties. This data provide a foundation for the development and optimization of structurally innovative antimicrobial drugs.
Collapse
Affiliation(s)
- Anjini Gayatri Akkiraju
- Molecular Medicine Lab, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India
| | - Aishwaraya Badugu
- Molecular Medicine Lab, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India
| | - Aditi Das
- Molecular Medicine Lab, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India
| | - Someswar Rao Sagurthi
- Molecular Medicine Lab, Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India
| |
Collapse
|
82
|
Vassiliev P, Gusev E, Komelkova M, Kochetkov A, Dobrynina M, Sarapultsev A. Computational Analysis of CD46 Protein Interaction with SARS-CoV-2 Structural Proteins: Elucidating a Putative Viral Entry Mechanism into Human Cells. Viruses 2023; 15:2297. [PMID: 38140538 PMCID: PMC10747966 DOI: 10.3390/v15122297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
This study examines an unexplored aspect of SARS-CoV-2 entry into host cells, which is widely understood to occur via the viral spike (S) protein's interaction with human ACE2-associated proteins. While vaccines and inhibitors targeting this mechanism are in use, they may not offer complete protection against reinfection. Hence, we investigate putative receptors and their cofactors. Specifically, we propose CD46, a human membrane cofactor protein, as a potential putative receptor and explore its role in cellular invasion, acting possibly as a cofactor with other viral structural proteins. Employing computational techniques, we created full-size 3D models of human CD46 and four key SARS-CoV-2 structural proteins-EP, MP, NP, and SP. We further developed 3D models of CD46 complexes interacting with these proteins. The primary aim is to pinpoint the likely interaction domains between CD46 and these structural proteins to facilitate the identification of molecules that can block these interactions, thus offering a foundation for novel pharmacological treatments for SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Pavel Vassiliev
- Laboratory for Information Technology in Pharmacology and Computer Modeling of Drugs, Research Center for Innovative Medicines, Volgograd State Medical University, 39 Novorossiyskaya Street, Volgograd 400087, Russia;
| | - Evgenii Gusev
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 106 Pervomaiskaya Street, Yekaterinburg 620049, Russia; (E.G.); (M.D.)
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 76 Lenin Prospekt, Chelyabinsk 454080, Russia;
| | - Maria Komelkova
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 76 Lenin Prospekt, Chelyabinsk 454080, Russia;
| | - Andrey Kochetkov
- Laboratory for Information Technology in Pharmacology and Computer Modeling of Drugs, Research Center for Innovative Medicines, Volgograd State Medical University, 39 Novorossiyskaya Street, Volgograd 400087, Russia;
| | - Maria Dobrynina
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 106 Pervomaiskaya Street, Yekaterinburg 620049, Russia; (E.G.); (M.D.)
| | - Alexey Sarapultsev
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 106 Pervomaiskaya Street, Yekaterinburg 620049, Russia; (E.G.); (M.D.)
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 76 Lenin Prospekt, Chelyabinsk 454080, Russia;
| |
Collapse
|
83
|
Akkiraju AG, Atcha KR, Sagurthi SR. Cloning, Purification, and Biophysical Characterization of FemB Protein from Methicillin-Resistant Staphylococcus aureus and Inhibitors Screening. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04780-8. [PMID: 37991634 DOI: 10.1007/s12010-023-04780-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2023] [Indexed: 11/23/2023]
Abstract
Methicillin-resistant Staphylococcus aureus has emerged as a leading cause of nosocomial, community acquired infections worldwide. Earlier investigations revealed that mecA-encoded FEM proteins play a role in antimicrobial resistance by developing unique peptidoglycan cross-linking which helps in the formation of protective cell membrane. In view to this, present study focused on expression, purification FEM proteins, and FemB biophysical characterization with the aid of in silico and in vitro approaches. Furthermore, we carried out biological screening assays and identified the novel potent 1,2,3-triazole conjugated 1,3,4-oxadiazole hybrid molecule which could inhibit the MRSA than the proven oxacillin.
Collapse
Affiliation(s)
- Anjini Gayatri Akkiraju
- Molecular Medicine Lab, Dept. of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India
| | - Krishnam Raju Atcha
- Department of Chemistry, Nizam College, Osmania University, Hyderabad, Telangana, 500001, India
| | - Someswar Rao Sagurthi
- Molecular Medicine Lab, Dept. of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana, 500007, India.
| |
Collapse
|
84
|
Srivastava D, Patra N. Enhanced Uptake of Anticancer C6-Pep Dimer in a Model Membrane Caused by Differential p Ka in Acidic Microenvironment. J Phys Chem B 2023; 127:9747-9758. [PMID: 37776281 DOI: 10.1021/acs.jpcb.3c04217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/02/2023]
Abstract
Acidic tumor microenvironment (TME) presents a challenge for the action of antitumor drugs by acting as an additional barrier for the passive crossing of the cell membrane by chemotherapic agents playing a critical role in the proliferation of tumor cells. Anticancer lipopeptide C6-Pep dimer containing the leucine zipper motif shows an increased uptake into the model tumor membrane in TME, and application of external heat might lead to the uncoiling of the zipper, which could result in cell lysis. This work investigated the cause of this increased uptake of C6-Pep dimer into the bilayer model in TME. Accurate protonation states of all the titratable residues of the C6-Pep dimer in TME were determined using constant pH molecular dynamics. In TME, except for two terminal Glu5 residues, all other Glu residues in the C6-Pep dimer were permanently protonated. The remaining Glu5 residues had differential pKa values, leading to the construction of four possible dimers with different fixed protonation states, and molecular dynamics was used to study their interaction with the anionic bilayer. Except for the dimer at a physiological pH, the other dimers were positively charged and could readily adsorb on the membrane surface. The free energy of insertion of these dimers in the bilayer was lower for single and double protonated Glu5-containing dimers than for the others. After the insertion of the lipopeptides into the membrane, thinning of the bilayer in the vicinity of dimers and an increase in area per lipid of the bilayer were observed for all systems, indicating destabilization of the bilayer due to this intercalation. This study shows that the anticancer lipopeptide C6-Pep utilizes the TME around a tumor cell for insertion into the membrane.
Collapse
Affiliation(s)
- Diship Srivastava
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| |
Collapse
|
85
|
Alibayov B, Scasny A, Vidal AGJ, Murin L, Wong S, Edwards KS, Eichembaun Z, Punshon T, Jackson BP, Hopp MT, McDaniel LS, Akerley BJ, Imhof D, Vidal JE. Oxidation of hemoglobin in the lung parenchyma facilitates the differentiation of pneumococci into encapsulated bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567109. [PMID: 38014009 PMCID: PMC10680745 DOI: 10.1101/2023.11.14.567109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Pneumococcal pneumonia causes cytotoxicity in the lung parenchyma but the underlying mechanism involves multiple factors contributing to cell death. Here, we discovered that hydrogen peroxide produced by Streptococcus pneumoniae (Spn-H 2 O 2 ) plays a pivotal role by oxidizing hemoglobin, leading to its polymerization and subsequent release of labile heme. At physiologically relevant levels, heme selected a population of encapsulated pneumococci. In the absence of capsule and Spn-H 2 O 2 , host intracellular heme exhibited toxicity towards pneumococci, thus acting as an antibacterial mechanism. Further investigation revealed that heme-mediated toxicity required the ABC transporter GlnPQ. In vivo experiments demonstrated that pneumococci release H 2 O 2 to cause cytotoxicity in bronchi and alveoli through the non-proteolytic degradation of intracellular proteins such as actin, tubulin and GAPDH. Overall, our findings uncover a mechanism of lung toxicity mediated by oxidative stress that favor the growth of encapsulated pneumococci suggesting a therapeutic potential by targeting oxidative reactions. Graphical abstract Highlights Oxidation of hemoglobin by Streptococcus pneumoniae facilitates differentiation to encapsulated pneumococci in vivo Differentiated S. pneumoniae produces capsule and hydrogen peroxide (Spn-H 2 O 2 ) as defense mechanism against host heme-mediated toxicity. Spn-H 2 O 2 -induced lung toxicity causes the oxidation and non-proteolytic degradation of intracellular proteins tubulin, actin, and GAPDH. The ABC transporter GlnPQ is a heme-binding complex that makes Spn susceptible to heme toxicity.
Collapse
|
86
|
Pereira GP, Jiménez-García B, Pellarin R, Launay G, Wu S, Martin J, Souza PCT. Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking. J Chem Inf Model 2023; 63:6823-6833. [PMID: 37877240 DOI: 10.1021/acs.jcim.3c01154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose interaction with the ubiquitination machinery leads to target degradation. This technology is emerging as an exciting new avenue for therapeutic development, with several PROTACs currently undergoing clinical trials targeting cancer. Here, we describe a general and computationally efficient methodology combining restraint-based docking, energy-based rescoring, and a filter based on the minimal solvent-accessible surface distance to produce PROTAC-compatible PPIs suitable for when there is no a priori known PROTAC ligand. In a benchmark employing a manually curated data set of 13 ternary complex crystals, we achieved an accuracy of 92% when starting from bound structures and 77% when starting from unbound structures, respectively. Our method only requires that the ligand-bound structures of the monomeric forms of the E3 ligase and target proteins be given to run, making it general, accurate, and highly efficient, with the ability to impact early-stage PROTAC-based drug design campaigns where no structural information about the ternary complex structure is available.
Collapse
Affiliation(s)
- Gilberto P Pereira
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | | | - Riccardo Pellarin
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Guillaume Launay
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Sangwook Wu
- PharmCADD, Busan 48792, Republic of Korea
- Department of Physics, Pukyong National University, Busan 48513, Republic of Korea
| | - Juliette Martin
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| |
Collapse
|
87
|
Rudd SR, Miranda LS, Curtis HR, Bigot Y, Diaz-Mendoza M, Hice R, Nizet V, Park HW, Blaha G, Federici BA, Bideshi DK. The Parasporal Body of Bacillus thuringiensis subsp. israelensis: A Unique Phage Capsid-Associated Prokaryotic Insecticidal Organelle. BIOLOGY 2023; 12:1421. [PMID: 37998020 PMCID: PMC10669011 DOI: 10.3390/biology12111421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
The three most important commercial bacterial insecticides are all derived from subspecies of Bacillus thuringiensis (Bt). Specifically, Bt subsp. kurstaki (Btk) and Bt subsp. aizawai (Bta) are used to control larval lepidopteran pests. The third, Bt subsp. israelensis (Bti), is primarily used to control mosquito and blackfly larvae. All three subspecies produce a parasporal body (PB) during sporulation. The PB is composed of insecticidal proteins that damage the midgut epithelium, initiating a complex process that results in the death of the insect. Among these three subspecies of Bt, Bti is unique as it produces the most complex PB consisting of three compartments. Each compartment is bound by a multilaminar fibrous matrix (MFM). Two compartments contain one protein each, Cry11Aa1 and Cyt1Aa1, while the third contains two, Cry4Aa1/Cry4Ba1. Each compartment is packaged independently before coalescing into the mature spherical PB held together by additional layers of the MFM. This distinctive packaging process is unparalleled among known bacterial organelles, although the underlying molecular biology is yet to be determined. Here, we present structural and molecular evidence that the MFM has a hexagonal pattern to which Bti proteins Bt152 and Bt075 bind. Bt152 binds to a defined spot on the MFM during the development of each compartment, yet its function remains unknown. Bt075 appears to be derived from a bacteriophage major capsid protein (MCP), and though its sequence has markedly diverged, it shares striking 3-D structural similarity to the Escherichia coli phage HK97 Head 1 capsid protein. Both proteins are encoded on Bti's pBtoxis plasmid. Additionally, we have also identified a six-amino acid motif that appears to be part of a novel molecular process responsible for targeting the Cry and Cyt proteins to their cytoplasmic compartments. This paper describes several previously unknown features of the Bti organelle, representing a first step to understanding the biology of a unique process of sorting and packaging of proteins into PBs. The insights from this research suggest a potential for future applications in nanotechnology.
Collapse
Affiliation(s)
- Sarah R. Rudd
- Program in Biomedical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA; (S.R.R.); (L.S.M.); (H.R.C.); (H.-W.P.)
- School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
- Department of Pediatrics, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA;
| | - Leticia Silva Miranda
- Program in Biomedical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA; (S.R.R.); (L.S.M.); (H.R.C.); (H.-W.P.)
| | - Hannah R. Curtis
- Program in Biomedical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA; (S.R.R.); (L.S.M.); (H.R.C.); (H.-W.P.)
- School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Yves Bigot
- UMR CNRS7247, Centre INRA Val de Loire, 37380 Nouzilly, France;
| | - Mercedes Diaz-Mendoza
- Department of Biochemistry and Molecular Biology, Faculty of Chemical and Biological Sciences, University Complutense of Madrid, 28040 Madrid, Spain;
| | - Robert Hice
- Department of Entomology, University of California, Riverside, CA 92521, USA;
| | - Victor Nizet
- Department of Pediatrics, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA;
| | - Hyun-Woo Park
- Program in Biomedical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA; (S.R.R.); (L.S.M.); (H.R.C.); (H.-W.P.)
| | - Gregor Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA;
| | - Brian A. Federici
- Department of Entomology, University of California, Riverside, CA 92521, USA;
| | - Dennis K. Bideshi
- Program in Biomedical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA; (S.R.R.); (L.S.M.); (H.R.C.); (H.-W.P.)
| |
Collapse
|
88
|
Arshad M, Noor N, Iqbal Z, Jaleel H. In silico analysis of missense SNPs in TNFR1a and their possible therapeutic or pathogenic role in immune diseases. Hum Immunol 2023; 84:609-617. [PMID: 37748952 DOI: 10.1016/j.humimm.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023]
Abstract
Tumor necrosis factor alpha (TNFa) is an inflammatory cytokine that is involved in the pathogenesis of various inflammatory disorders including rheumatoid arthritis. TNF-alpha receptor I (TNFR1a) is one of the receptors TNFa binds with for its activation. Any variation in this receptor might affect the role of TNFa in successive events. Amino acid residue substitutions might happen in TNFR1a through non-synonymous single nucleotide polymorphisms (nsSNPs) which may alter the functioning of TNFa, hence, identifying any such substitutions is of paramount significance. In this study, six nsSNPs at five different evolutionary conserved regions are predicted to be detrimental to the structure and/or function of TNFR1a by using numerous computational tools. Their 3D models are also proposed in this study. Besides, they were found to reduce the stability and affect the molecular mechanisms of this protein. Two contrasting possibilities might happen because of these substitutions. One, they might reduce the production of TNFa which is overexpressed in inflammatory diseases, hence can play therapeutic role in such diseases. Second, they might possibly hinder the apoptosis to occur which can effectuate the uncontrolled division of cells, hence can be pathogenic in diseases like cancer. Further investigations on these nsSNPs using animal models and at cellular level will open doors to understand the underlying mechanisms behind various diseases.
Collapse
Affiliation(s)
- Maria Arshad
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik, Iceland.
| | - Nabeel Noor
- Shalamar Medical & Dental College, Lahore, Pakistan
| | - Zunair Iqbal
- Shalamar Medical & Dental College, Lahore, Pakistan
| | - Hadiqa Jaleel
- Department of Research & Innovation, Shalamar Institute of Health Sciences, Lahore, Pakistan
| |
Collapse
|
89
|
Hayat C, Shahab M, Khan SA, Liang C, Duan X, Khan H, Zheng G, Ul-Haq Z. Design of a novel multiple epitope-based vaccine: an immunoinformatics approach to combat monkeypox. J Biomol Struct Dyn 2023; 41:9344-9355. [PMID: 36331082 PMCID: PMC9718376 DOI: 10.1080/07391102.2022.2141887] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Monkeypox virus is an infectious agent that causes fever, Pneumonitis encephalitis, rash, lymphadenopathy and bacterial infection. The current outbreak of monkeypox has reawakened the global health concern. In the current situation of increasing viral infection, no vaccine or drug is available for monkeypox. Thus, there is an urgent need for viable vaccine development to prevent viral transmission by boosting human immunity. Herein, using immunoinformatics approaches, a multi-epitope vaccine was constructed for the Monkeypox virus. In this connection, B-Cell and T-cell epitopes were identified and joined with the help of adjutants and linkers. The vaccine construct was selected based on promising vaccine candidates and immunogenic potential. Further epitopes were selected based on antigenicity score, non-allergenicity and good immunological properties. Molecular docking reveals strong interactions between TLR-9 and the predicted vaccine construct. Finally, molecular dynamics simulations were performed to evaluate the stability and compactness of the constructed vaccine. The MD simulation results demonstrated the significant stability of the polypeptide vaccine construct. The predicted vaccine represented good stability, expression, immunostimulatory capabilities and significant solubility. Design vaccine was verified as efficient in different computer-based immune response investigations. Additionally, the constructed vaccine also represents a good population coverage in computer base analysis.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Chandni Hayat
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul Wali Khan University, Mardan, Pakistan
| | - Muhammad Shahab
- State Key Laboratories Of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Salman Ali Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Chaoqun Liang
- State Key Laboratories Of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Xiuyuan Duan
- State Key Laboratories Of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Haleema Khan
- Department of Chemistry, UCSS, Abdul Wali Khan University, Mardan, Pakistan
| | - Guojun Zheng
- State Key Laboratories Of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| |
Collapse
|
90
|
Zhu HT, Xia YH, Zhang GJ. E2EDA: Protein Domain Assembly Based on End-to-End Deep Learning. J Chem Inf Model 2023; 63:6451-6461. [PMID: 37788318 DOI: 10.1021/acs.jcim.3c01387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
With the development of deep learning, almost all single-domain proteins can be predicted at experimental resolution. However, the structure prediction of multi-domain proteins remains a challenge. Achieving end-to-end protein domain assembly and further improving the accuracy of the full-chain modeling by accurately predicting inter-domain orientation while improving the assembly efficiency will provide significant insights into structure-based drug discovery. In this work, we propose an End-to-End Domain Assembly method based on deep learning, named E2EDA. We first develop RMNet, an EfficientNetV2-based deep learning model that fuses multiple features using an attention mechanism to predict inter-domain rigid motion. Then, the predicted rigid motions are transformed into inter-domain spatial transformations to directly assemble the full-chain model. Finally, the scoring strategy RMscore is designed to select the best model from multiple assembled models. The experimental results show that the average TM-score of the model assembled by E2EDA on the benchmark set (282) is 0.827, which is better than those of other domain assembly methods SADA (0.792) and DEMO (0.730). Meanwhile, on our constructed multi-domain data set from AlphaFold DB, the model reassembled by E2EDA is 7.0% higher in TM-score compared to the full-chain model predicted by AlphaFold2, indicating that E2EDA can capture more accurate inter-domain orientations to improve the quality of the model predicted by AlphaFold2. Furthermore, compared to SADA and AlphaFold2, E2EDA reduced the average runtime on the benchmark by 64.7% and 19.2%, respectively, indicating that E2EDA can significantly improve assembly efficiency through an end-to-end approach. The online server is available at http://zhanglab-bioinf.com/E2EDA.
Collapse
Affiliation(s)
- Hai-Tao Zhu
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China
| | - Yu-Hao Xia
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China
| | - Gui-Jun Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China
| |
Collapse
|
91
|
Zraly CB, Schultz R, Diaz MO, Dingwall AK. New twists of a TAIL: novel insights into the histone binding properties of a highly conserved PHD finger cluster within the MLR family of H3K4 mono-methyltransferases. Nucleic Acids Res 2023; 51:9672-9689. [PMID: 37638761 PMCID: PMC10570056 DOI: 10.1093/nar/gkad698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/19/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023] Open
Abstract
Enhancer activation by the MLR family of H3K4 mono-methyltransferases requires proper recognition of histones for the deposition of the mono-methyl mark. MLR proteins contain two clusters of PHD zinc finger domains implicated in chromatin regulation. The second cluster is the most highly conserved, preserved as an ancient three finger functional unit throughout evolution. Studies of the isolated 3rd PHD finger within this cluster suggested specificity for the H4 [aa16-20] tail region. We determined the histone binding properties of the full three PHD finger cluster b module (PHDb) from the Drosophila Cmi protein which revealed unexpected recognition of an extended region of H3. Importantly, the zinc finger spacer separating the first two PHDb fingers from the third is critical for proper alignment and coordination among fingers for maximal histone engagement. Human homologs, MLL3 and MLL4, also show conservation of H3 binding, expanding current views of histone recognition for this class of proteins. We further implicate chromatin remodeling by the SWI/SNF complex as a possible mechanism for the accessibility of PHDb to globular regions of histone H3 beyond the tail region. Our results suggest a two-tail histone recognition mechanism by the conserved PHDb domain involving a flexible hinge to promote interdomain coordination.
Collapse
Affiliation(s)
- Claudia B Zraly
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Richard Schultz
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Manuel O Diaz
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Andrew K Dingwall
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| |
Collapse
|
92
|
Yajnik KN, Gupta SRR, Taneja M, Singh IK, Singh A. Deciphering mitogen activated protein kinase pathway activated during insect attack in Nicotiana attenuata. J Biomol Struct Dyn 2023:1-17. [PMID: 37811559 DOI: 10.1080/07391102.2023.2263795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023]
Abstract
Plant yields are compromised due to abiotic and biotic stresses. A crucial biotic stress instigated by insect attack, is a major concern that limits crop production. To overcome the deleterious effect of herbivory, pesticides are used but long-term usage of pesticides can be harmful to the environment and human health. Understanding the plants' inherent defense mechanism by interpreting the interaction pattern of defense-related proteins and signalling components and manipulating them to strengthen defense status, is one of the alternative approaches of green biotechnology. During insect attack, host plants initiate innumerable signalling pathways to activate defense response; Mitogen Activated Protein Kinase (MAPK) Pathway is a crucial component of signalling pathway that regulate the expression of downstream defense-related genes. MAPK pathway has three components: MAPKKK, MAPKK and MAPK. Earlier studies have shown participation of SIPK and WIPK (MAPKs) as well as MEK2 (MAPKK) during insect infestation and its association with plant defense. However, information on the third component and elucidation of the complete MAPK pathway are still elusive. Therefore, this study aims to identify the unknown component and decipher MAPK pathway in Nicotiana attenuata involved in plant defense against herbivory by identifying herbivory-inducible MAPKKKs and and their interaction with known partners of the MAPK pathway by docking and MD simulation. The possible pathway was predicted to be MAPKKK Na12134/Na04522-MEK2-SIPK/WIPK. Further, validation of the above interaction by in vitro and in vivo methods is highly recommended.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Kalpesh Nath Yajnik
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
| | - Shradheya R R Gupta
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| | - Mansi Taneja
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India
| |
Collapse
|
93
|
Ali G, Sadia S, Ain-ul- Batool S, Azeem Z, Awan NB, Kazmi SAR, Ur- Rehman Z, Anjum Z, Ur- Rehman F, Wali A, Khan K, Zaman N, Ayub M, Sajid M, Hassan N. A Recurrent Nonsense Mutation in NECTIN4 Underlying Ectodermal Dysplasia-Syndactyly Syndrome with a Novel Phenotype in a Consanguineous Kashmiri Family. Genet Res (Camb) 2023; 2023:9999660. [PMID: 37829154 PMCID: PMC10567209 DOI: 10.1155/2023/9999660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 10/14/2023] Open
Abstract
EDSS1, a syndrome characterized by ectodermal dysplasia-syndactyly, is inherited in an autosomal recessive manner due to mutations in the NECTIN4/PVRL4 gene. Clinical manifestations of the syndrome include defective nail plate, sparse to absent scalp and body hair, spaced teeth with enamel hypoplasia, and bilateral cutaneous syndactyly in the fingers and toes. Here, we report a consanguineous family of Kashmiri origin presenting features of EDSS1. Using whole exome sequencing, we found a recurrent nonsense mutation (NM_030916: c.181C > T, p.(Gln61 ∗)) in the NECTIN4 gene. The variant segregated perfectly with the disorder within the family. The candidate variant was absent in 50 in-house exomes pertaining to other disorders from the same population. In addition to the previously reported clinical phenotype, an upper lip cleft was found in one of the affected members as a novel phenotype that is not reported by previous studies in EDSS1 patients. Therefore, the study presented here, which was conducted on the Kashmiri population, is the first to document a NECTIN4 mutation associated with the upper lip cleft as a novel phenotype. This finding broadens the molecular and phenotypic spectrum of EDSS1.
Collapse
Affiliation(s)
- Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sadia Sadia
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Syeda Ain-ul- Batool
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Zahid Azeem
- Department of Biochemistry, Azad Jammu and Kashmir Medical College, Muzaffarabad, Pakistan
| | - Naheed Bashir Awan
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | | | - Zia- Ur- Rehman
- Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Zeeshan Anjum
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Fazal- Ur- Rehman
- Department of Microbiology, Faculty of Life Sciences, University of Balochistan, Quetta, Pakistan
| | - Abdul Wali
- Department of Biotechnology, Faculty of Life Sciences and Informatics, BUITEMS, 87100, Quetta, Pakistan
| | - Kafaitullah Khan
- Department of Microbiology, Faculty of Life Sciences, University of Balochistan, Quetta, Pakistan
| | - Nasib Zaman
- Centre for Biotechnology and Microbiology University of Swat, Swat, Pakistan
| | - Muhammad Ayub
- Institute of Biochemistry, University of Balochistan, Quetta, Pakistan
| | - Muhammad Sajid
- Department of Pathology, College of Veterinary and Animal Sciences, Jhang Sub Campus of University of Veterinary and Animal Sciences Lahore, Lahore, Pakistan
| | - Noor Hassan
- Institute of Biochemistry, University of Balochistan, Quetta, Pakistan
| |
Collapse
|
94
|
Liu J, Liu D, Zhang GJ. DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes. Bioinformatics 2023; 39:btad591. [PMID: 37740296 PMCID: PMC10560100 DOI: 10.1093/bioinformatics/btad591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/21/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023] Open
Abstract
MOTIVATION Model quality assessment is a crucial part of protein structure prediction and a gateway to proper usage of models in biomedical applications. Many methods have been proposed for assessing the quality of structural models of protein monomers, but few methods for evaluating protein complex models. As protein complex structure prediction becomes a new challenge, there is an urgent need for model quality assessment methods that can accurately assess the accuracy of interface residues of complex structures. RESULTS Here, we present DeepUMQA3, a web server for evaluating the accuracy of interface residues of protein complex structures using deep neural networks. For an input complex structure, features are extracted from three levels of overall complex, intra-monomer, and inter-monomer, and an improved deep residual neural network is used to predict per-residue lDDT and interface residue accuracy. DeepUMQA3 ranks first in the blind test of interface residue accuracy estimation in CASP15, with Pearson, Spearman, and AUC of 0.564, 0.535, and 0.755 under the lDDT measurement, which are 17.6%, 23.6%, and 10.9% higher than the second best method, respectively. DeepUMQA3 can also assess the accuracy of all residues in the entire complex and distinguish high- and low-precision residues. AVAILABILITY AND IMPLEMENTATION The web sever of DeepUMQA3 are freely available at http://zhanglab-bioinf.com/DeepUMQA_server/.
Collapse
Affiliation(s)
- Jun Liu
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Dong Liu
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Gui-Jun Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| |
Collapse
|
95
|
Petrzik K, Brázdová S. Jojan: a novel virus that lyses Stenotrophomonas maltophilia from dog. Virus Genes 2023; 59:775-780. [PMID: 37458918 DOI: 10.1007/s11262-023-02021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Stenotrophomonas maltophilia is a Gram-negative bacterium widely distributed in the environment and associated with nosocomial infections, pneumonia, and bacteremia in humans and other mammals. We have isolated and sequenced a new virus that lyses the S. maltophilia strain from a dog skin. The virus has a siphovirus-like morphology and a linear dsDNA genome 60,804 pb in length with terminal repeats, four tRNA genes, and 111 putative proteins. The annotated genes resemble the corresponding genes of some siphoviruses, but the unique genome arrangement and limited similarity of the encoded proteins suggest that this virus does not belong to any known genus. The virus uses zinc metallopeptidase for lysis of its host. This enzyme is active in the presence of Zn2+ or Mg2+ ions and maintains its bactericidal activity up to 50 °C. Both the virus itself and the endolysin specifically degrade only the host bacterial strain.
Collapse
Affiliation(s)
- Karel Petrzik
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Sára Brázdová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| |
Collapse
|
96
|
Wu Y, Li Y, Chu W, Niu T, Feng X, Ma R, Liu H. Expression and functional characterization of odorant-binding protein 2 in the predatory mite Neoseiulus barkeri. INSECT SCIENCE 2023; 30:1493-1506. [PMID: 36458978 DOI: 10.1111/1744-7917.13156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Olfaction plays a crucial role for arthropods in foraging, mating, and oviposition. The odorant-binding protein (OBP) gene is considered one of the most important olfactory genes. However, little is known about its functions in predatory mites. Here, we used Neoseiulus barkeri, an important commercialized natural pest control, to explore the chemosensory characteristics of OBP. In this study, N. barkeri was attracted by methyl salicylate (MeSA) and showed higher crawling speeds under MeSA treatment. Then, we identified and cloned an OBP gene named Nbarobp2 and analyzed its expression profiles in the predatory mite. Nbarobp2 was 663 bp, was highly expressed in larval and nymphal stages, and was significantly upregulated in N. barkeri under MeSA treatment. Nbarobp2 encoded 202 amino acid residues with a molecular weight of 23 kDa (after removing the signal peptide). Sequence comparisons revealed that the OBPs in Arachnida shared 6 conserved cysteine sites, but were distinguishable from the OBPs of Insecta on the phylogenetic tree. RNA interference, Western blotting, and binding affinity assays further proved that Nbarobp2 was involved in volatile perception in predatory mites. This study shed light on the functional characteristics of OBPs in predatory mites, providing a new insight for better biological control.
Collapse
Affiliation(s)
- Yixia Wu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Beibei District, Chongqing, 400715, China
| | - Yaying Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Beibei District, Chongqing, 400715, China
| | - Wenqiang Chu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Beibei District, Chongqing, 400715, China
| | - Tiandi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Beibei District, Chongqing, 400715, China
| | - Xiaotian Feng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Beibei District, Chongqing, 400715, China
| | - Rongjiang Ma
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Beibei District, Chongqing, 400715, China
| | - Huai Liu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Beibei District, Chongqing, 400715, China
| |
Collapse
|
97
|
Tan M, Xia J, Luo H, Meng G, Zhu Z. Applying the digital data and the bioinformatics tools in SARS-CoV-2 research. Comput Struct Biotechnol J 2023; 21:4697-4705. [PMID: 37841328 PMCID: PMC10568291 DOI: 10.1016/j.csbj.2023.09.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023] Open
Abstract
Bioinformatics has been playing a crucial role in the scientific progress to fight against the pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The advances in novel algorithms, mega data technology, artificial intelligence and deep learning assisted the development of novel bioinformatics tools to analyze daily increasing SARS-CoV-2 data in the past years. These tools were applied in genomic analyses, evolutionary tracking, epidemiological analyses, protein structure interpretation, studies in virus-host interaction and clinical performance. To promote the in-silico analysis in the future, we conducted a review which summarized the databases, web services and software applied in SARS-CoV-2 research. Those digital resources applied in SARS-CoV-2 research may also potentially contribute to the research in other coronavirus and non-coronavirus viruses.
Collapse
Affiliation(s)
- Meng Tan
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jiaxin Xia
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Haitao Luo
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Geng Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhenglin Zhu
- School of Life Sciences, Chongqing University, Chongqing, China
| |
Collapse
|
98
|
Zhuang X, Xiao R, Fu Y, Yang B, Fan J, Lu F, Qin T, Yang X, Hu X, Yin J, Li W, Kang X, Chen G, Hu D, Sun C. MRE11:p.K464R mutation mediates olaparib resistance by enhancing DNA damage repair in HGSOC. Cell Biosci 2023; 13:178. [PMID: 37759323 PMCID: PMC10537967 DOI: 10.1186/s13578-023-01117-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Although the clinical application of PARP inhibitors has brought hope to ovarian cancer, the problem of its resistance has become increasingly prominent. Therefore, clinical experts have been focused on finding specific indicators and therapeutic targets that can be used for resistance monitoring of PARP inhibitors. RESULTS By cfDNA detecting during Olaparib maintenance therapy in platinum-sensitive relapsed ovarian cancer, we found the presence of MRE11:p.K464R mutation was strongly associated with acquired Olaparib resistance. Structural analysis revealed that the MRE11:p.K464R mutation is situated at a critical site where the MRE11 protein interacts with other biomolecules, leading to potential structural and functional abnormalities of MRE11 protein. Functionally, MRE11:p.K464R mutation enhanced the tolerance of Olaparib by reducing the DNA damage. Mechanistically, MRE11:p.K464R mutation improved the efficiency of DNA damage repair and induce Olaparib resistance by enhancing its binding activity with the interacting proteins (including RAD50 and RPS3). Among them, the enhanced binding of MRE11:p.K464R mutation to RAD50/RPS3 facilitated non-homologous end joining (NHEJ) repair in tumor cells, thereby expanding the scope of research into acquired resistance to PARP inhibitors. CONCLUSIONS Our findings provide a theoretical basis for MRE11:p.K464R mutation as a specific indicator of resistance monitoring in Olaparib treatment, and the exploration of its resistance mechanism provides a novel insights for the formulation of combination ther therapies after Olaparib resistance.
Collapse
Affiliation(s)
- Xucui Zhuang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rourou Xiao
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Fu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Yang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junpeng Fan
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Funian Lu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tianyu Qin
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohang Yang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xingyuan Hu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingjing Yin
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenting Li
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyan Kang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gang Chen
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dianxing Hu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Chaoyang Sun
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
99
|
Thongchol J, Lill Z, Hoover Z, Zhang J. Recent Advances in Structural Studies of Single-Stranded RNA Bacteriophages. Viruses 2023; 15:1985. [PMID: 37896763 PMCID: PMC10610835 DOI: 10.3390/v15101985] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Positive-sense single-stranded RNA (ssRNA) bacteriophages (phages) were first isolated six decades ago. Since then, extensive research has been conducted on these ssRNA phages, particularly those infecting E. coli. With small genomes of typically 3-4 kb that usually encode four essential proteins, ssRNA phages employ a straightforward infectious cycle involving host adsorption, genome entry, genome replication, phage assembly, and host lysis. Recent advancements in metagenomics and transcriptomics have led to the identification of ~65,000 sequences from ssRNA phages, expanding our understanding of their prevalence and potential hosts. This review article illuminates significant investigations into ssRNA phages, with a focal point on their structural aspects, providing insights into the various stages of their infectious cycle.
Collapse
Affiliation(s)
| | | | | | - Junjie Zhang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; (J.T.); (Z.L.); (Z.H.)
| |
Collapse
|
100
|
Fan Y, Peng F, Cui R, Wang S, Cui Y, Lu X, Huang H, Ni K, Liu X, Jiang T, Feng X, Liu M, Lei Y, Chen W, Meng Y, Han M, Wang D, Yin Z, Chen X, Wang J, Li Y, Guo L, Zhao L, Ye W. GhIMP10D, an inositol monophosphates family gene, enhances ascorbic acid and antioxidant enzyme activities to confer alkaline tolerance in Gossypium hirsutum L. BMC PLANT BIOLOGY 2023; 23:447. [PMID: 37736713 PMCID: PMC10515029 DOI: 10.1186/s12870-023-04462-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND Inositol monophosphates (IMP) are key enzymes in the ascorbic acid (AsA) synthesis pathways, which play vital roles in regulating plant growth and development and stresses tolerance. To date, no comprehensive analysis of the expression profile of IMP genes and their functions under abiotic stress in cotton has been reported. RESULTS In this study, the genetic characteristics, phylogenetic evolution, cis-acting elements and expression patterns of IMP gene family in cotton were systematically analyzed. A total of 28, 27, 13 and 13 IMP genes were identified in Gossypium hirsutum (G. hirsutum), Gossypium barbadense (G. barbadense), Gossypium arboreum (G. arboreum), and Gossypium raimondii (G. raimondii), respectively. Phylogenetic analysis showed that IMP family genes could cluster into 3 clades. Structure analysis of genes showed that GhIMP genes from the same subgroup had similar genetic structure and exon number. And most GhIMP family members contained hormone-related elements (abscisic acid response element, MeJA response element, gibberellin response element) and stress-related elements (low temperature response element, defense and stress response element, wound response element). After exogenous application of abscisic acid (ABA), some GhIMP genes containing ABA response elements positively responded to alkaline stress, indicating that ABA response elements played an important role in response to alkaline stress. qRT-PCR showed that most of GhIMP genes responded positively to alkaline stress, and GhIMP10D significantly upregulated under alkaline stress, with the highest up-regulated expression level. Virus-induced gene silencing (VIGS) experiment showed that compared with 156 plants, MDA content of pYL156:GhIMP10D plants increased significantly, while POD, SOD, chlorophyII and AsA content decreased significantly. CONCLUSIONS This study provides a thorough overview of the IMP gene family and presents a new perspective on the evolution of this gene family. In particular, some IMP genes may be involved in alkaline stress tolerance regulation, and GhIMP10D showed high expression levels in leaves, stems and roots under alkaline stress, and preliminary functional verification of GhIMP10D gene suggested that it may regulate tolerance to alkaline stress by regulating the activity of antioxidant enzymes and the content of AsA. This study contributes to the subsequent broader discussion of the structure and alkaline resistance of IMP genes in cotton.
Collapse
Affiliation(s)
- Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Fanjia Peng
- Hunan Institute of Cotton Science, Hunan, 415101, China
| | - Ruifeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Yupeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Hui Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Kesong Ni
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Xiaoyu Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Tiantian Jiang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Xixian Feng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Mengyue Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Yuqian Lei
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Wenhua Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Yuan Meng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Zujun Yin
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Yujun Li
- Hunan Institute of Cotton Science, Hunan, 415101, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Institute of Technology, Henan, 455000, China.
| |
Collapse
|