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Sahoo S, Son S, Lee HK, Lee JY, Gosu V, Shin D. Impact of nsSNPs in human AIM2 and IFI16 gene: a comprehensive in silico analysis. J Biomol Struct Dyn 2024; 42:2603-2615. [PMID: 37139544 DOI: 10.1080/07391102.2023.2206907] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/19/2023] [Indexed: 05/05/2023]
Abstract
AIM2 and IFI16 are the most studied members of AIM2-like receptors (ALRs) in humans and share a common N-Terminal PYD domain and C-terminal HIN domain. The HIN domain binds to dsDNA in response to the invasion of bacterial and viral DNA, and the PYD domain directs apoptosis-associated speck-like protein via protein-protein interactions. Hence, activation of AIM2 and IFI16 is crucial for protection against pathogenic assaults, and any genetic variation in these inflammasomes can dysregulate the human immune system. In this study, different computational tools were used to identify the most deleterious and disease-causing non-synonymous single nucleotide polymorphisms (nsSNPs) in AIM2 and IFI16 proteins. Molecular dynamic simulation was performed for the top damaging nsSNPs to study single amino acid substitution-induced structural alterations in AIM2 and IFI16. The observed results suggest that the variants G13V, C304R, G266R, and G266D for AIM2, and G13E and C356F are deleterious and affect structural integrity. We hope that the suggested deleterious nsSNPs and structural dynamics of AIM2 and IFI16 variants will guide future research to better understand the function of these variants with large-scale studies and may assist in fresher therapeutics focusing on these polymorphisms.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sthitaprajna Sahoo
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Seungwoo Son
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hak-Kyo Lee
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Jun-Yeong Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Vijayakumar Gosu
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
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2
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Murthy TPK, Shukla R, Durga Prasad N, Swetha P, Shreyas S, Singh TR, Pattabiraman R, Nair SS, Mathew BB, Kumar KM. Comprehensive analysis of non-synonymous missense SNPs of human galactose mutarotase (GALM) gene: an integrated computational approach. J Biomol Struct Dyn 2023; 41:11178-11192. [PMID: 36591702 DOI: 10.1080/07391102.2022.2160813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/15/2022] [Indexed: 01/03/2023]
Abstract
Missense Non-synonymous single nucleotide polymorphisms (nsSNPs) of Galactose Mutarotase (GALM) are associated with the Novel type of Galactosemia (Galactosemia type 4) together with symptoms such as high blood galactose levels and eye cataracts. The objective of the present study was to identify deleterious nsSNPs of GALM recorded on the dbSNP database through comprehensive insilico analysis. Among the 319 missense nsSNPs reported, various insilco tools predicted R78S, R82G, A163E, P210S, Y281C, E307G and F339C as the most deleterious mutations. Structural analysis, PTM analysis and molecular dynamics simulations (MDS) were carried out to understand the effect of these mutations on the structural and physicochemical properties of the GALM protein. The residues R82G and E307G were found to be part of the binding site that resulted in decreased surface accessibility. Replacing the charged wild-type residue with a neutral mutant type affected its substrate binding. All 7 mutations were found to increase the rigidity of the protein structure, which is unfavorable during ligand binding. The mutation F339E made the protein structure more rigid than all the other mutations. Y281 is a phosphorylated site, and therefore, less significant structural changes were observed when compared to other mutations; however, it may have significant differences in the usual functioning of the protein. In summary, the structural and functional analysis of missense SNPs of GALM is important to reduce the number of potential mutations to be evaluated in vitro to understand the association with some genetic diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- T P Krishna Murthy
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - N Durga Prasad
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Praveen Swetha
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - S Shreyas
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Ramya Pattabiraman
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Shishira S Nair
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Blessy B Mathew
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, Karnataka, Inida
| | - K M Kumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
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Naseri M, Niazi A, Bagherzadeh K, Konoz E, Samadikhah HR. Modified electrochemical aptasensor for ultrasensitive detection of tetracycline: In silico and in vitro studies. Food Chem 2023; 421:136195. [PMID: 37119689 DOI: 10.1016/j.foodchem.2023.136195] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/15/2023] [Accepted: 04/16/2023] [Indexed: 05/01/2023]
Abstract
An ultrasensitive electrochemical aptasensor based on a glassy carbon electrode, modified by carbon nanofibers and carboxylated multi-walled carbon nanotubes was fabricated to detect tetracycline in food samples. The affinity of antibiotics, including kanamycin, tetracycline, ampicillin, and sulfadimethoxine toward desired sequences of aptamers and the stability of antibiotic-aptamer complexes were studied using molecular docking and molecular dynamic simulations. Moreover, the highest affinity and most stable complex were observed for tetracycline in complex with kanamycin-specific aptamer (KAP). Finally, KAP was used to develop an aptasensor. The central composite design (CCD) was used to optimize effective parameters. The biosensor achieved a wide dynamic linear range (1.0 × 10-17-1.0 × 10-5 M) and a low limit of detection (2.28 × 10-18 M) under optimized conditions using differential pulse voltammetry. Using the developed aptasensor, tetracycline residues in milk samples were determined.
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Affiliation(s)
- Masoomeh Naseri
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Ali Niazi
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran.
| | - Kowsar Bagherzadeh
- Eye Research Center, Five Senses Health Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran; Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Elahe Konoz
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Hamid Reza Samadikhah
- Department of Fundamental, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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Al-Khannaq M, Lytton J. Regulation of K +-Dependent Na +/Ca 2+-Exchangers (NCKX). Int J Mol Sci 2022; 24:ijms24010598. [PMID: 36614039 PMCID: PMC9820825 DOI: 10.3390/ijms24010598] [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: 12/05/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022] Open
Abstract
Potassium-dependent sodium-calcium exchangers (NCKX) have emerged as key determinants of calcium (Ca2+) signaling and homeostasis, especially in environments where ion concentrations undergo large changes, such as excitatory cells and transport epithelia. The regulation of NCKX transporters enables them to respond to the changing cellular environment thereby helping to shape the extent and kinetics of Ca2+ signals. This review examines the current knowledge of the different ways in which NCKX activity can be modulated. These include (i) cellular and dynamic subcellular location (ii); changes in protein expression mediated at the gene, transcript, or protein level (iii); genetic changes resulting in altered protein structure or expression (iv); regulation via changes in substrate concentration (v); and post-translational modification, partner protein interactions, and allosteric regulation. Detailed mechanistic understanding of NCKX regulation is an emerging area of research with the potential to provide important new insights into transporter function, the control of Ca2+ signals, and possible interventions for dysregulated Ca2+ homeostasis.
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Chear CT, Mat Ripen A, Mohamad SB. Deciphering the structural and functional impact of Q657L mutation in NLRC4 using computational methods. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2080822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Chai Teng Chear
- Primary Immunodeficiency Unit, Allergy and Immunology Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Selangor, Malaysia
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Adiratna Mat Ripen
- Primary Immunodeficiency Unit, Allergy and Immunology Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Selangor, Malaysia
| | - Saharuddin Bin Mohamad
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
- Centre of Research in Systems Biology, Structural Bioinformatics and Human Digital Imaging (CRYSTAL), Universiti Malaya, Kuala Lumpur, Malaysia
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Taghvaei S, Sabouni F, Minuchehr Z. Identification of Natural Products as SENP2 Inhibitors for Targeted Therapy in Heart Failure. Front Pharmacol 2022; 13:817990. [PMID: 35431915 PMCID: PMC9012495 DOI: 10.3389/fphar.2022.817990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Aims: Sentrin-specific protease -2 (SENP2) is involved in deSUMOylation. Increased deSUMOylation in murine hearts by SENP2 upregulation resulted in cardiac dysfunction and congenital heart defects. Natural compounds via regulating cell proliferation and survival, induce cell cycle cessation, cell death, apoptosis, and producing reactive oxygen species and various enzyme systems cause disease prevention. Then, natural compounds can be suitable inhibitors and since SENP2 is a protein involved in heart disease, so our aim was inhibition of SENP2 by natural products for heart disease treatment. Material and methods: Molecular docking and molecular dynamics simulation of natural products i.e. Gallic acid (GA), Caffeic acid (CA), Thymoquinone (TQ), Betanin, Betanidin, Fisetin, and Ebselen were done to evaluate the SENP2 inhibitory effect of these natural products. The toxicity of compounds was also predicted. Results: The results showed that Betanin constituted a stable complex with SENP2 active site as it revealed low RMSD, high binding energy, and hydrogen bonds. Further, as compared to Ebselen, Betanin demonstrated low toxicity, formed a stable complex with SENP2 via four to seven hydrogen bonds, and constituted more stable MD plots. Therefore, depending upon the outcomes presented herein, Betanin significantly inhibited SENP2 and hence may be considered as a suitable natural compound for the treatment of heart failure. Further clinical trials must be conducted to validate its use as a potential SENP2 inhibitor.
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Affiliation(s)
- Somayye Taghvaei
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Farzaneh Sabouni
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
- *Correspondence: Farzaneh Sabouni, ; Zarrin Minuchehr,
| | - Zarrin Minuchehr
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
- *Correspondence: Farzaneh Sabouni, ; Zarrin Minuchehr,
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Ammar A, Cavill R, Evelo C, Willighagen E. PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow. J Cheminform 2022; 14:8. [PMID: 35227289 PMCID: PMC8886843 DOI: 10.1186/s13321-021-00573-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/18/2021] [Indexed: 11/15/2022] Open
Abstract
A key concept in drug design is how natural variants, especially the ones occurring in the binding site of drug targets, affect the inter-individual drug response and efficacy by altering binding affinity. These effects have been studied on very limited and small datasets while, ideally, a large dataset of binding affinity changes due to binding site single-nucleotide polymorphisms (SNPs) is needed for evaluation. However, to the best of our knowledge, such a dataset does not exist. Thus, a reference dataset of ligands binding affinities to proteins with all their reported binding sites' variants was constructed using a molecular docking approach. Having a large database of protein-ligand complexes covering a wide range of binding pocket mutations and a large small molecules' landscape is of great importance for several types of studies. For example, developing machine learning algorithms to predict protein-ligand affinity or a SNP effect on it requires an extensive amount of data. In this work, we present PSnpBind: A large database of 0.6 million mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow. It provides a web interface to explore and visualize the protein-ligand complexes and a REST API to programmatically access the different aspects of the database contents. PSnpBind is open source and freely available at https://psnpbind.org .
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Affiliation(s)
- Ammar Ammar
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Rachel Cavill
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Chris Evelo
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Egon Willighagen
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
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Das R, Kundu S, Laskar S, Choudhury Y, Ghosh SK. In silico assessment of DNA damage response gene variants associated with head and neck cancer. J Biomol Struct Dyn 2022; 41:2090-2107. [PMID: 35037836 DOI: 10.1080/07391102.2022.2027817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Head and neck cancer (HNC), the sixth most common cancer globally, stands first in India, especially Northeast India, where tobacco usage is predominant, which introduces various carcinogens leading to malignancies by accumulating DNA damages. Consequently, the present work aimed to predict the impact of significant germline variants in DNA repair and Tumour Suppressor genes on HNC development. WES in Ion ProtonTM platform on 'discovery set' (n = 15), followed by recurrence assessment of the observed variants on 'confirmation set' (n = 40) using Sanger Sequencing was performed on the HNC-prevalent NE Indian populations. Initially, 53 variants were identified, of which seven HNC-linked DNA damage response gene variants were frequent in the studied populations. Different tools ascertained the biological consequences of these variants, of which the non-coding variants viz. EXO1_rs4150018, RAD52_rs6413436, CHD5_rs2746066, HACE1_rs6918700 showed risk, while FLT3_rs2491227 and BMPR1A_rs7074064 conferred protection against HNC by affecting transcriptional regulation and splicing mechanism. Molecular Dynamics Simulation of the full-length p53 model predicted that the observed coding TP53_rs1042522 variant conferred HNC-risk by altering the structural dynamics of the protein, which displayed difficulty in the transition between active and inactive conformations due to high-energy barrier. Subsequent pathway and gene ontology analysis revealed that EXO1, RAD52 and TP53 variants affected the Double-Strand Break Repair pathway, whereas CHD5 and HACE1 variants inactivated DNA repair cascade, facilitating uncontrolled cell proliferation, impaired apoptosis and malignant transformation. Conversely, FLT3 and BMPR1A variants protected against HNC by controlling tumorigenesis, which requires experimental validation. These findings may serve as prognostic markers for developing preventive measures against HNC.
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Affiliation(s)
- Raima Das
- Department of Biotechnology, Assam University, Silchar, India
| | - Sharbadeb Kundu
- Genome Science, School of Interdisciplinary Studies, University of Kalyani, Nadia, West India
| | - Shaheen Laskar
- Department of Biotechnology, Assam University, Silchar, India
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Mousivand M, Bagherzadeh K, Anfossi L, Javan-Nikkhah M. Key criteria for engineering mycotoxin binding aptamers via computational simulations: Aflatoxin B1 as a case study. Biotechnol J 2021; 17:e2100280. [PMID: 34800084 DOI: 10.1002/biot.202100280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 12/30/2022]
Abstract
Due to the difficulties in monoclonal antibody production specific to mycotoxins, aptameric probes have been considered as suitable alternatives. The low efficiency of the SELEX procedure in screening high affinity aptamers for binding mycotoxins as small molecules can be significantly improved through computational techniques. Previously, we designed five new aptamers to aflatoxin B1 (AFB1) based on a known aptamer sequence (Patent: PCT/CA2010/001 292, Apt1) through a genetic algorithm-based in silico maturation strategy and experimentally measured their affinity to the target toxin. Here, integrated molecular dynamic simulation (MDs) studies with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis to clarify the binding modes, critical interacting nucleic bases and energy component contributions in the six AFB1-binding aptamers. The aptamer F20, which was selected in the first work, showed the best free binding energy and complex stability compared to other aptamers. The trajectory analysis revealed that AFB1 recognized F20 through the groove binding mode along with precise shape complementarity. The MD simulation results revealed that dynamic water intermediate interactions also play a key role in promoting complex stability. According to the MM-PBSA calculations, van der Waals contacts were identified as dominant energy components in all complexes. Interestingly, a high consistency is observed between the experimentally obtained binding affinities of the six aptamers with their free energy solvation. The computational findings, confirmed via previous experiments, highlighted the binding modes, the dynamic hydration of complex components and the total free interacting energy as the crucial criteria in discovering high functional aptameric probes.
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Affiliation(s)
- Maryam Mousivand
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Kowsar Bagherzadeh
- Stem Cell and Regenerative Medicine Research Center, Iran University of Medical Sciences, Eye Research Center, the Five Senses Health Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Laura Anfossi
- Department of Chemistry, University of Turin, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Turin, Italy
| | - Mohammad Javan-Nikkhah
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Department of Plant Protection, College of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
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Computational Analysis of Gly482Ser Single-Nucleotide Polymorphism in PPARGC1A Gene Associated with CAD, NAFLD, T2DM, Obesity, Hypertension, and Metabolic Diseases. PPAR Res 2021; 2021:5544233. [PMID: 34394332 PMCID: PMC8360745 DOI: 10.1155/2021/5544233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022] Open
Abstract
Peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PPARGC1A) regulates the expression of energy metabolism's genes and mitochondrial biogenesis. The essential roles of PPARGC1A encouraged the researchers to assess the relation between metabolism-related diseases and its variants. To study Gly482Ser (+1564G/A) single-nucleotide polymorphism (SNP) after PPARGC1A modeling, we substitute Gly482 for Ser482. Stability prediction tools showed that this substitution decreases the stability of PPARGC1A or has a destabilizing effect on this protein. We then utilized molecular dynamics simulation of both the Gly482Ser variant and wild type of the PPARGC1A protein to analyze the structural changes and to reveal the conformational flexibility of the PPARGC1A protein. We observed loss flexibility in the RMSD plot of the Gly482Ser variant, which was further supported by a decrease in the SASA value in the Gly482Ser variant structure of PPARGC1A and an increase of H-bond with the increase of β-sheet and coil and decrease of turn in the DSSP plot of the Gly482Ser variant. Such alterations may significantly impact the structural conformation of the PPARGC1A protein, and it might also affect its function. It showed that the Gly482Ser variant affects the PPARGC1A structure and makes the backbone less flexible to move. In general, molecular dynamics simulation (MDS) showed more flexibility in the native PPARGC1A structure. Essential dynamics (ED) also revealed that the range of eigenvectors in the conformational space has lower extension of motion in the Gly482Ser variant compared with WT. The Gly482Ser variant also disrupts PPARGC1A interaction. Due to this single-nucleotide polymorphism in PPARGC1A, it became more rigid and might disarray the structural conformation and catalytic function of the protein and might also induce type 2 diabetes mellitus (T2DM), coronary artery disease (CAD), and nonalcoholic fatty liver disease (NAFLD). The results obtained from this study will assist wet lab research in expanding potent treatment on T2DM.
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11
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Novel structural and functional impact of damaging single nucleotide polymorphisms (SNPs) on human SMYD2 protein using computational approaches. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Galeb HA, Wilkinson EL, Stowell AF, Lin H, Murphy ST, Martin‐Hirsch PL, Mort RL, Taylor AM, Hardy JG. Melanins as Sustainable Resources for Advanced Biotechnological Applications. GLOBAL CHALLENGES (HOBOKEN, NJ) 2021; 5:2000102. [PMID: 33552556 PMCID: PMC7857133 DOI: 10.1002/gch2.202000102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/04/2020] [Indexed: 05/17/2023]
Abstract
Melanins are a class of biopolymers that are widespread in nature and have diverse origins, chemical compositions, and functions. Their chemical, electrical, optical, and paramagnetic properties offer opportunities for applications in materials science, particularly for medical and technical uses. This review focuses on the application of analytical techniques to study melanins in multidisciplinary contexts with a view to their use as sustainable resources for advanced biotechnological applications, and how these may facilitate the achievement of the United Nations Sustainable Development Goals.
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Affiliation(s)
- Hanaa A. Galeb
- Department of ChemistryLancaster UniversityLancasterLA1 4YBUK
- Department of ChemistryScience and Arts CollegeRabigh CampusKing Abdulaziz UniversityJeddah21577Saudi Arabia
| | - Emma L. Wilkinson
- Department of Biomedical and Life SciencesLancaster UniversityLancasterLA1 4YGUK
| | - Alison F. Stowell
- Department of Organisation, Work and TechnologyLancaster University Management SchoolLancaster UniversityLancasterLA1 4YXUK
| | - Hungyen Lin
- Department of EngineeringLancaster UniversityLancasterLA1 4YWUK
| | - Samuel T. Murphy
- Department of EngineeringLancaster UniversityLancasterLA1 4YWUK
- Materials Science InstituteLancaster UniversityLancasterLA1 4YBUK
| | - Pierre L. Martin‐Hirsch
- Lancashire Teaching Hospitals NHS TrustRoyal Preston HospitalSharoe Green LanePrestonPR2 9HTUK
| | - Richard L. Mort
- Department of Biomedical and Life SciencesLancaster UniversityLancasterLA1 4YGUK
| | - Adam M. Taylor
- Lancaster Medical SchoolLancaster UniversityLancasterLA1 4YWUK
| | - John G. Hardy
- Department of ChemistryLancaster UniversityLancasterLA1 4YBUK
- Materials Science InstituteLancaster UniversityLancasterLA1 4YBUK
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Akın-Balı DF, Al-Khafaji K, Aktas SH, Taskin-Tok T. Bioinformatic and computational analysis for predominant mutations of the Nrf2/Keap1 complex in pediatric leukemia. J Biomol Struct Dyn 2020; 39:4290-4303. [PMID: 32469262 DOI: 10.1080/07391102.2020.1775702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The levels of reactive oxygen species (ROS) are tightly controlled and regulated by Nuclear Factor Erythroid-2-Like 2 (Nrf2) transcription factor, which is the main regulator of antioxidant responses and its suppressor protein Kelch-like ECH-associated protein 1 (Keap1). Our previous study has identified six novel changes in Nrf2/Keap1 pathway in pediatric ALL, which were described for the first time. These changes in the pathway are likely to alter the evolutionary process of amino acids and cause structural changes in the final products of genes. In this study, we aimed to compare the pathogenicity of eight determined mutations reported in our previous study by utilizing different programs with different algorithms and molecular dynamics simulation. Since it is too difficult to handle each existing mutation in a wet laboratory, in silico methods may give suggestion to choose the important mutations for further analysis and to establish the appropriate patient population and conduct wet laboratory studies. For this purpose, four different algorithms were used to evaluate the effects of single amino acid mutation. In addition, root-mean-square deviation, root-mean-square fluctuation and free-energy landscape analyses were performed to observe stability, flexibility and energetically favorable conformations, respectively, for each amino acid mutation. As a result, our study emphasizes the importance of Keap1 mutations in pediatric ALL Nrf2/Keap1 pathway, a total of eight mutations, two of which were shown for the first time in our study. Especially the mutations in the Keap1 Broad-Complex, Tramtrack and Bric-à-brac domain are worthy of attention.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dilara Fatma Akın-Balı
- Faculty of Medicine, Department of Medical Biology, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Khattab Al-Khafaji
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey
| | - Sedef Hande Aktas
- Vocational School of Health Services, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Tugba Taskin-Tok
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey.,Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey
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Wang Q, Mehmood A, Wang H, Xu Q, Xiong Y, Wei DQ. Computational Screening and Analysis of Lung Cancer Related Non-Synonymous Single Nucleotide Polymorphisms on the Human Kirsten Rat Sarcoma Gene. Molecules 2019; 24:molecules24101951. [PMID: 31117243 PMCID: PMC6572712 DOI: 10.3390/molecules24101951] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/18/2019] [Accepted: 05/19/2019] [Indexed: 11/16/2022] Open
Abstract
The human KRAS (Kirsten rat sarcoma) is an oncogene, involved in the regulation of cell growth and division. The mutations in the KRAS gene have the potential to cause normal cells to become cancerous in human lungs. In the present study, we focus on non-synonymous single nucleotide polymorphisms (nsSNPs), which are point mutations in the DNA sequence leading to the amino acid variants in the encoded protein. To begin with, we developed a pipeline to utilize a set of computational tools in order to obtain the most deleterious nsSNPs (Q22K, Q61P, and Q61R) associated with lung cancer in the human KRAS gene. Furthermore, molecular dynamics simulation and structural analyses of the 3D structures of native and mutant proteins confirmed the impact of these nsSNPs on the stability of the protein. Finally, the experimental results demonstrated that the structural stability of the mutant proteins was worse than that of the native protein. This study provides significant guidance for narrowing down the number of KRAS mutations to be screened as potential diagnostic biomarkers and to better understand the structural and functional mechanisms of the KRAS protein.
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Affiliation(s)
- Qiankun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Aamir Mehmood
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Heng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yi Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Bao Y, Zhou L, Dai D, Zhu X, Hu Y, Qiu Y. Discover potential inhibitors for PFKFB3 using 3D-QSAR, virtual screening, molecular docking and molecular dynamics simulation. J Recept Signal Transduct Res 2019; 38:413-431. [PMID: 30822195 DOI: 10.1080/10799893.2018.1564150] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 (PFKFB3) is a master regulator of glycolysis in cancer cells by synthesizing fructose-2,6-bisphosphate (F-2,6-BP), a potent allosteric activator of phosphofructokinase-1 (PFK-1), which is a rate-limiting enzyme of glycolysis. PFKFB3 is an attractive target for cancer treatment. It is valuable to discover promising inhibitors by using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking and molecular dynamics simulation. Twenty molecules with known activity were used to build 3D-QSAR pharmacophore models. The best pharmacophore model was ADHR called Hypo1, which had the highest correlation value of 0.98 and the lowest RMSD of 0.82. Then, the Hypo1 was validated by cost value method, test set method and decoy set validation method. Next, the Hypo1 combined with Lipinski's rule of five and ADMET properties were employed to screen databases including Asinex and Specs, total of 1,048,159 molecules. The hits retrieved from screening were docked into protein by different procedures including HTVS, SP and XP. Finally, nine molecules were picked out as potential PFKFB3 inhibitors. The stability of PFKFB3-lead complexes was verified by 40 ns molecular dynamics simulation. The binding free energy and the energy contribution of per residue to the binding energy were calculated by MM-PBSA based on molecular dynamics simulation.
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Affiliation(s)
- Yinfeng Bao
- a College of Chemical Engineering , Sichuan University , Chengdu , China
| | - Lu Zhou
- a College of Chemical Engineering , Sichuan University , Chengdu , China
| | - Duoqian Dai
- a College of Chemical Engineering , Sichuan University , Chengdu , China
| | - Xiaohong Zhu
- a College of Chemical Engineering , Sichuan University , Chengdu , China
| | - Yanqiu Hu
- a College of Chemical Engineering , Sichuan University , Chengdu , China
| | - Yaping Qiu
- a College of Chemical Engineering , Sichuan University , Chengdu , China
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