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Szafron LA, Iwanicka-Nowicka R, Podgorska A, Bonna AM, Sobiczewski P, Kupryjanczyk J, Szafron LM. The Clinical Significance of CRNDE Gene Methylation, Polymorphisms, and CRNDEP Micropeptide Expression in Ovarian Tumors. Int J Mol Sci 2024; 25:7531. [PMID: 39062774 PMCID: PMC11277161 DOI: 10.3390/ijms25147531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
CRNDE is an oncogene expressed as a long non-coding RNA. However, our team previously reported that the CRNDE gene also encodes a micropeptide, CRNDEP. The amino acid sequence of CRNDEP has recently been revealed by other researchers, too. This study aimed to investigate genetic alterations within the CRNDEP-coding region of the CRNDE gene, methylation profiling of this gene, and CRNDEP expression analysis. All investigations were performed on clinical material from patients with ovarian tumors of diverse aggressiveness. We found that CRNDEP levels were significantly elevated in highly aggressive tumors compared to benign neoplasms. Consistently, a high level of this micropeptide was a negative, independent, prognostic, and predictive factor in high-grade ovarian cancer (hgOvCa) patients. The cancer-promoting role of CRNDE(P), shown in our recent study, was also supported by genetic and epigenetic results obtained herein, revealing no CRNDEP-disrupting mutations in any clinical sample. Moreover, in borderline ovarian tumors (BOTS), but not in ovarian cancers, the presence of a single nucleotide polymorphism in CRNDE, rs115515594, significantly increased the risk of recurrence. Consistently, in BOTS only, the same genetic variant was highly overrepresented compared to healthy individuals. We also discovered that hypomethylation of CRNDE is associated with increased aggressiveness of ovarian tumors. Accordingly, hypomethylation of this gene's promoter/first exon correlated with hgOvCa resistance to chemotherapy, but only in specimens with accumulation of the TP53 tumor suppressor protein. Taken together, these results contribute to a better understanding of the role of CRNDE(P) in tumorigenesis and potentially may lead to improvements in screening, diagnosis, and treatment of ovarian neoplasms.
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Affiliation(s)
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Agnieszka Podgorska
- Cancer Molecular and Genetic Diagnostics Department, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | | | - Piotr Sobiczewski
- Department of Gynecological Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Jolanta Kupryjanczyk
- Department of Cancer Pathomorphology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland;
| | - Lukasz Michal Szafron
- Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
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2
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Qin X, Chen B. Comprehensive analysis and validation reveal potential MYCN regulatory biomarkers associated with neuroblastoma prognosis. J Biomol Struct Dyn 2023; 41:8902-8917. [PMID: 36300516 DOI: 10.1080/07391102.2022.2138977] [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: 05/30/2022] [Accepted: 10/16/2022] [Indexed: 10/31/2022]
Abstract
Neuroblastoma (NB) is an embryonic malignant tumor that occurs in the sympathetic nervous system. The treatment results of patients in the high-risk group are poor, and relapse and treatment failure can occur even with multiple combination treatments. The proto-oncogene MYCN is a BHLH Transcription Factor used as an independent prognostic factor for NB. The proportion of MYCN amplification in tumor tissues of high-risk patients reaches 40-50%. Hence, exploring new MYCN target genes is a meaningful approach in developing treatment for high-risk NB patients. The microarray datasets were obtained from Gene Expression Omnibus (GEO), and differentially expressed genes (DEGs) were identified. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and miRPathDB were used for enrichment analysis. STRING and Cytoscape were used to construct a protein-protein interaction (PPI) network and for modular analysis. The miRNet and NetworkAnalyst databases were used to predict and construct gene-miRNA and gene-TFs networks. The R2 database was used for expression, correlation, and prognostic analyses. The diagnostic value of the biomarkers was predicted by ROC analysis, and RT-qPCR was used to validate the identified hub genes. Finally, using specific MYCN siRNA and overexpressing plasmids, the correlation between the identified hub genes and MYCN was investigated. Our results showed that FBXO9, HECW2, MIB2, RNF19B, RNF213, TRIM36, and ZBTB16 are novel biomarkers that affect the prognosis of the NB patients. In addition, FBXO9, RNF19B, and TRIM36 were preliminarily confirmed as potential target genes of MYCN. Overall, FBXO9, HECW2, MIB2, RNF19B, RNF213, TRIM36, and ZBTB16 are expected to become novel biomarkers for the treatment of high-risk NB patients.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xiuni Qin
- Guangzhou Concord Cancer Center, Guangzhou, China
| | - Bo Chen
- Medical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
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3
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Xu G, van Bruggen R, Gualtieri CO, Moradin N, Fois A, Vallerand D, De Sa Tavares Russo M, Bassenden A, Lu W, Tam M, Lesage S, Girouard H, Avizonis DZ, Deblois G, Prchal JT, Stevenson M, Berghuis A, Muir T, Rabinowitz J, Vidal SM, Fodil N, Gros P. Bisphosphoglycerate Mutase Deficiency Protects against Cerebral Malaria and Severe Malaria-Induced Anemia. Cell Rep 2020; 32:108170. [PMID: 32966787 DOI: 10.1016/j.celrep.2020.108170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 07/07/2020] [Accepted: 08/27/2020] [Indexed: 11/30/2022] Open
Abstract
The replication cycle and pathogenesis of the Plasmodium malarial parasite involves rapid expansion in red blood cells (RBCs), and variants of certain RBC-specific proteins protect against malaria in humans. In RBCs, bisphosphoglycerate mutase (BPGM) acts as a key allosteric regulator of hemoglobin/oxyhemoglobin. We demonstrate here that a loss-of-function mutation in the murine Bpgm (BpgmL166P) gene confers protection against both Plasmodium-induced cerebral malaria and blood-stage malaria. The malaria protection seen in BpgmL166P mutant mice is associated with reduced blood parasitemia levels, milder clinical symptoms, and increased survival. The protective effect of BpgmL166P involves a dual mechanism that enhances the host's stress erythroid response to Plasmodium-driven RBC loss and simultaneously alters the intracellular milieu of the RBCs, including increased oxyhemoglobin and reduced energy metabolism, reducing Plasmodium maturation, and replication. Overall, our study highlights the importance of BPGM as a regulator of hemoglobin/oxyhemoglobin in malaria pathogenesis and suggests a new potential malaria therapeutic target.
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Affiliation(s)
- Guoyue Xu
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada
| | - Rebekah van Bruggen
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Christian O Gualtieri
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Neda Moradin
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada
| | - Adrien Fois
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Diane Vallerand
- Université de Montréal, Département de Pharmacologie et Physiologie, Pav Roger-Gaudry, 2900 Édouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | | | - Angelia Bassenden
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Mifong Tam
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Sylvie Lesage
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Hélène Girouard
- Université de Montréal, Département de Pharmacologie et Physiologie, Pav Roger-Gaudry, 2900 Édouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - Daina Zofija Avizonis
- Rosalind and Morris Goodman Cancer Research Centre, 1160 Pin Avenue West, Montréal, QC H3A 1A3, Canada
| | - Geneviève Deblois
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Faculté de Pharmacie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Josef T Prchal
- Division of Hematology, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - Mary Stevenson
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Albert Berghuis
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Tom Muir
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Joshua Rabinowitz
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Silvia M Vidal
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Nassima Fodil
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada; Centre CERMO-FC Pavillon des Sciences Biologiques, 141 Avenue du Président Kennedy, Montréal, QC H2X 3Y7, Canada.
| | - Philippe Gros
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada.
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Otani N, Sugano K, Inami S, Amano H, Arikawa T, Saito S, Imai K, Ushiama M, Yoshida T, Kimura N, Toyoda S, Inoue T. Cardiac paraganglioma with a novel germline mutation of succinate dehydrogenase gene D. Jpn J Clin Oncol 2018; 47:1193-1197. [PMID: 28977582 DOI: 10.1093/jjco/hyx132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/25/2017] [Indexed: 11/14/2022] Open
Abstract
A 58-year-old woman with a past medical history of a carotid body tumor, resected 4 months prior to presentation, was admitted to our hospital for treatment of a cardiac tumor that was identified on post-operative echocardiography and chest computed tomography. The cardiac tumor was surgically removed and identified pathologically as a paraganglioma, similarly to the carotid body tumor. Genetic analysis of both tumors identified a non-synonymous mutation in the succinate dehydrogenase (SDH) gene D, Exon4, c.320T>C, p.Leu107Pro showing co-segregation with paternal transmission and maternal imprinting among family members. This novel mutation appears to be the cause of familial paraganglioma in this patient.
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Affiliation(s)
- Naoyuki Otani
- Department of Cardiovascular Medicine Dokkyo Medical University
| | - Kokichi Sugano
- Oncogene Res Unit/Cancer Prevention Unit, Tochigi Cancer Center Research Institute
| | - Shu Inami
- Department of Cardiovascular Medicine Dokkyo Medical University
| | - Hirohisa Amano
- Department of Cardiovascular Medicine Dokkyo Medical University
| | - Takuo Arikawa
- Department of Cardiovascular Medicine Dokkyo Medical University
| | - Shinya Saito
- Oncogene Res Unit/Cancer Prevention Unit, Tochigi Cancer Center Research Institute
| | - Kazuho Imai
- Oncogene Res Unit/Cancer Prevention Unit, Tochigi Cancer Center Research Institute
| | - Mineko Ushiama
- Division of Genetics, National Cancer Center Research Institute
| | - Teruhiko Yoshida
- Department of Genetic Medicine and Services, National Cancer Center Hospital
| | - Noriko Kimura
- Department of Clinical Research, Pathology Section, National Hospital Organization, Hakodate Hospital, Japan
| | - Shigeru Toyoda
- Department of Cardiovascular Medicine Dokkyo Medical University
| | - Teruo Inoue
- Department of Cardiovascular Medicine Dokkyo Medical University
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5
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Helicobacter pylori Adapts to Chronic Infection and Gastric Disease via pH-Responsive BabA-Mediated Adherence. Cell Host Microbe 2017; 21:376-389. [PMID: 28279347 DOI: 10.1016/j.chom.2017.02.013] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/16/2016] [Accepted: 02/17/2017] [Indexed: 01/22/2023]
Abstract
The BabA adhesin mediates high-affinity binding of Helicobacter pylori to the ABO blood group antigen-glycosylated gastric mucosa. Here we show that BabA is acid responsive-binding is reduced at low pH and restored by acid neutralization. Acid responsiveness differs among strains; often correlates with different intragastric regions and evolves during chronic infection and disease progression; and depends on pH sensor sequences in BabA and on pH reversible formation of high-affinity binding BabA multimers. We propose that BabA's extraordinary reversible acid responsiveness enables tight mucosal bacterial adherence while also allowing an effective escape from epithelial cells and mucus that are shed into the acidic bactericidal lumen and that bio-selection and changes in BabA binding properties through mutation and recombination with babA-related genes are selected by differences among individuals and by changes in gastric acidity over time. These processes generate diverse H. pylori subpopulations, in which BabA's adaptive evolution contributes to H. pylori persistence and overt gastric disease.
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6
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Heaton MP, Smith TPL, Carnahan JK, Basnayake V, Qiu J, Simpson B, Kalbfleisch TS. Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertension. F1000Res 2016; 5:2003. [PMID: 27746904 PMCID: PMC5040160 DOI: 10.12688/f1000research.9254.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 01/08/2023] Open
Abstract
The availability of whole genome sequence (WGS) data has made it possible to discover protein variants
in silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in global beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene (
EPAS1), a gene associated with pulmonary hypertension in Angus cattle. The identity and quality of genomic sequences were verified by comparing WGS genotypes to those derived from other methods. The average read depth, genotype scoring rate, and genotype accuracy exceeded 14, 99%, and 99%, respectively. The 96 genomes were used to discover four amino acid variants encoded by
EPAS1 (E270Q, P362L, A671G, and L701F) and confirm two variants previously associated with disease (A606T and G610S). The six
EPAS1 missense mutations were verified with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assays, and their frequencies were estimated in a separate collection of 1154 U.S. cattle representing 46 breeds. A rooted phylogenetic tree of eight polypeptide sequences provided a framework for evaluating the likely order of mutations and potential impact of
EPAS1 alleles on the adaptive response to chronic hypoxia in U.S. cattle. This public, whole genome resource facilitates
in silico identification of protein variants in diverse types of U.S. beef cattle, and provides a means of translating WGS data into a practical biological and evolutionary context for generating and testing hypotheses.
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Affiliation(s)
| | | | | | | | | | | | - Theodore S Kalbfleisch
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, USA
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7
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Heaton MP, Smith TP, Carnahan JK, Basnayake V, Qiu J, Simpson B, Kalbfleisch TS. Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertension. F1000Res 2016; 5:2003. [PMID: 27746904 PMCID: PMC5040160 DOI: 10.12688/f1000research.9254.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 08/24/2023] Open
Abstract
The availability of whole genome sequence (WGS) data has made it possible to discover protein variants in silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in global beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene ( EPAS1), a gene associated with pulmonary hypertension in Angus cattle. The identity and quality of genomic sequences were verified by comparing WGS genotypes to those derived from other methods. The average read depth, genotype scoring rate, and genotype accuracy exceeded 14, 99%, and 99%, respectively. The 96 genomes were used to discover four amino acid variants encoded by EPAS1 (E270Q, P362L, A671G, and L701F) and confirm two variants previously associated with disease (A606T and G610S). The six EPAS1 missense mutations were verified with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assays, and their frequencies were estimated in a separate collection of 1154 U.S. cattle representing 46 breeds. A rooted phylogenetic tree of eight polypeptide sequences provided a framework for evaluating the likely order of mutations and potential impact of EPAS1 alleles on the adaptive response to chronic hypoxia in U.S. cattle. This public, whole genome resource facilitates in silico identification of protein variants in diverse types of U.S. beef cattle, and provides a means of translating WGS data into a practical biological and evolutionary context for generating and testing hypotheses.
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Affiliation(s)
| | | | | | | | | | | | - Theodore S. Kalbfleisch
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, USA
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Vinay Kumar C, Kumar KM, Swetha R, Ramaiah S, Anbarasu A. Protein aggregation due to nsSNP resulting in P56S VABP protein is associated with amyotrophic lateral sclerosis. J Theor Biol 2014; 354:72-80. [PMID: 24681403 DOI: 10.1016/j.jtbi.2014.03.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/14/2014] [Accepted: 03/16/2014] [Indexed: 12/13/2022]
Abstract
Mutations in the gene encoding vesicle-associated membrane protein (VAPB) cause amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. The VAPB gene is mapped to chromosome number 20 and can be found at cytogenetic location 20q13.33 of the chromosome. VAPB is seen to play a significant role in the unfolded protein response (UPR), which is a process that suppresses the accumulation of unfolded proteins in the endoplasmic reticulum. Earlier studies have reported two points; which we have analyzed in our study. Firstly, the mutation P56S in the VAPB is seen to increase the stability of the protein and secondly, the mutation P56S in VAPB is seen to interrupt the functioning of the gene and loses its ability to be involved in the activation of the IRE1/XBP1 pathway which leads to ALS. With correlation on the previous research studies on the stability of this protein, we carried out Molecular dynamics (MD) simulation. We analyzed the SNP results of 17 nsSNPs obtained from dbSNP using SIFT, polyphen, I-Mutant, SNP&GO, PhDSNP and Mutpred to predict the role of nsSNPs in VAPB. MD simulation is carried out and plots for RMSD, RMSF, Rg, SASA, H-bond and PCA are obtained to check and prove the stability of the wild type and the mutant protein structure. The protein is checked for its aggregation and the results obtained show changes in the protein structure that might result in the loss of function.
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Affiliation(s)
- Chundi Vinay Kumar
- School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - K M Kumar
- School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Rayapadi Swetha
- School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Sudha Ramaiah
- School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Anand Anbarasu
- School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India.
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