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Xu H, Xu D, Liu Y. Molecular Biology Applications of Psychrophilic Enzymes: Adaptations, Advantages, Expression, and Prospective. Appl Biochem Biotechnol 2024:10.1007/s12010-023-04810-5. [PMID: 38183603 DOI: 10.1007/s12010-023-04810-5] [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: 12/09/2023] [Indexed: 01/08/2024]
Abstract
Psychrophilic enzymes are primarily produced by microorganisms from extremely low-temperature environments which are known as psychrophiles. Their high efficiency at low temperatures and easy heat inactivation property have attracted extensive attention from various food and industrial bioprocesses. However, the application of these enzymes in molecular biology is still limited. In a previous review, the applications of psychrophilic enzymes in industries such as the detergent additives, the food additives, the bioremediation, and the pharmaceutical medicine, and cosmetics have been discussed. In this review, we discuss the main cold adaptation characteristics of psychrophiles and psychrophilic enzymes, as well as the relevant information on different psychrophilic enzymes in molecular biology. We summarize the mining and screening methods of psychrophilic enzymes. We finally recap the expression of psychrophilic enzymes. We aim to provide a reference process for the exploration and expression of new generation of psychrophilic enzymes.
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Affiliation(s)
- Hu Xu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Dawei Xu
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Yongqin Liu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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2
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Aghaei S, Parvizpour S, Farrokhi E, Molavi N, Hoseinzadeh M, Tabatabaiefar MA. Characterization of a novel androgen receptor gene variant identified in an Iranian family with complete androgen insensitivity syndrome (CAIS): a molecular dynamics simulation study. J Biomol Struct Dyn 2023; 41:9850-9864. [PMID: 36411944 DOI: 10.1080/07391102.2022.2148125] [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: 05/30/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022]
Abstract
Androgen insensitivity syndrome (AIS) is a common form of 46, XY disorder in sex development disease (DSD). It is due to the androgen receptor (AR) gene mutations and includes clinical subgroups of complete AIS (CAIS) and partial AIS (PAIS), along with a vast area of clinical heterogeneity of completely normal female external genitalia to male infertility. In this study, the Whole Exome Sequencing (WES) was utilized to detect the cause of DSD in a consanguineous Iranian family with two female patients with normal external genitalia and 46, XY karyotype. Sanger sequencing was applied to validate the candidate variant. Next, we predicted the structural alteration induced by the variant on AR protein using bioinformatics analysis such as molecular dynamic (MD) and molecular docking simulations. WES results identified a novel hemizygous p.L763V variant in the AR gene in the proband that was compatible with the X-linked recessive pattern of inheritance. Bioinformatics studies confirmed the loss of AR function. Based on the American College of Medical Genetics and Genomics (ACMG) guidelines, it was categorized as pathogenic. This study broadens the AR mutation spectrum and introduces the novel p.L763V missense pathogenic variant leading to AR failure to bind to its ligand, and the resulting CAIS clinical subgroup. This study presents a prosperous application of WES and bioinformatics analysis to recognize the underlying cause of DSD in Iran, necessary for its clinical/psychological management.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shahrzad Aghaei
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Sepideh Parvizpour
- Research center for Pharmaceutical Nanotechnology, Biomedicine Institute Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Effat Farrokhi
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Newsha Molavi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Marziyeh Hoseinzadeh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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3
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Hadizadeh M, AminJafari A, Parvizpour S, Ghasemi S. Novel targets to overcome antiangiogenesis therapy resistance in glioblastoma multiforme: Systems biology approach and suggestion of therapy by galunisertib. Cell Biol Int 2022; 46:1649-1660. [PMID: 35842773 DOI: 10.1002/cbin.11859] [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] [Received: 01/19/2022] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 11/06/2022]
Abstract
Glioblastoma multiforme (GBM) is a tumor with high microvessel density. Antiangiogenesis therapy (AAT) resistance occurs due to the complex mechanisms involved in angiogenesis, with increased chances of recurrence. The vascular endothelial growth factor (VEGF) pathway is the main pathway of angiogenesis, and anti-VEGF drugs have been ineffective in controlling it. New oncogenes in the VEGF signaling pathway may be new candidates for angiogenesis targeting. Oncogene candidates were chosen using gene expression profiles and databases. Then oncogenes were subjected to gene set enrichment analysis (GSEA) and survival analysis (SA). Molecular docking was conducted to evaluate the interaction of the oncogenes with galunisertib. NRAS, AKT1, and HSPB1 were the most effective oncogenes upregulating genes that play a role in GBM expression in the VEGF signaling pathway. The VEGF and MAPK signaling pathways were found to be effective using GSEA and Kyoto Encyclopedia Gene and Genome pathway analysis. Survival analyses revealed that patients with high HSPB1 expression had poorer overall survival rates than those with low HSPB1 expression. Galunisertib exhibits intermolecular interactions with 6DV5, 5UHV, and 3O96 (binding energy -8.0, -8.6, and -10.3 kcal/mol, respectively). The current AAT should be restrategized to suppress the numerous angiogenic elements to manage angiogenesis and combat AAT resistance in GBM. In silico analysis indicated that NRAS, AKT1, and HSPB1 genes can be the main oncogenes in the VEGF signaling pathway and galunisertib strongly interacts with these genes. Consequently, the use of galunisertib to overcome AAT in GBM in combination therapy can be assessed.
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Affiliation(s)
- Morteza Hadizadeh
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Akram AminJafari
- Cellular and Molecular Research Center, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sorayya Ghasemi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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4
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Kim DY, Kim J, Lee YM, Byeon SM, Gwak JH, Lee JS, Shin DH, Park HY. Novel, acidic, and cold-adapted glycoside hydrolase family 8 endo-β-1,4-glucanase from an Antarctic lichen-associated bacterium, Lichenicola cladoniae PAMC 26568. Front Microbiol 2022; 13:935497. [PMID: 35910630 PMCID: PMC9329076 DOI: 10.3389/fmicb.2022.935497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Endo-β-1,4-glucanase is a crucial glycoside hydrolase (GH) involved in the decomposition of cellulosic materials. In this study, to discover a novel cold-adapted β-1,4-D-glucan-degrading enzyme, the gene coding for an extracellular endo-β-1,4-glucanase (GluL) from Lichenicola cladoniae PAMC 26568, an Antarctic lichen (Cladonia borealis)-associated bacterium, was identified and recombinantly expressed in Escherichia coli BL21. The GluL gene (1044-bp) encoded a non-modular polypeptide consisting of a single catalytic GH8 domain, which shared the highest sequence identity of 55% with that of an uncharacterized protein from Gluconacetobacter takamatsuzukensis (WP_182950054). The recombinant endo-β-1,4-glucanase (rGluL: 38.0 kDa) most efficiently degraded sodium carboxymethylcellulose (CMC) at pH 4.0 and 45°C, and showed approximately 23% of its maximum degradation activity even at 3°C. The biocatalytic activity of rGluL was noticeably enhanced by >1.3-fold in the presence of 1 mM Mn2+ or NaCl at concentrations between 0.1 and 0.5 M, whereas the enzyme was considerably downregulated by 1 mM Hg2+ and Fe2+ together with 5 mM N-bromosuccinimide and 0.5% sodium dodecyl sulfate. rGluL is a true endo-β-1,4-glucanase, which could preferentially decompose D-cellooligosaccharides consisting of 3 to 6 D-glucose, CMC, and barley β-glucan, without other additional glycoside hydrolase activities. The specific activity (15.1 U mg-1) and k cat/K m value (6.35 mg-1 s-1mL) of rGluL toward barley β-glucan were approximately 1.8- and 2.2-fold higher, respectively, compared to its specific activity (8.3 U mg-1) and k cat/K m value (2.83 mg-1 s-1mL) toward CMC. The enzymatic hydrolysis of CMC, D-cellotetraose, and D-cellohexaose yielded primarily D-cellobiose, accompanied by D-glucose, D-cellotriose, and D-cellotetraose. However, the cleavage of D-cellopentaose by rGluL resulted in the production of only D-cellobiose and D-cellotriose. The findings of the present study imply that rGluL is a novel, acidic, and cold-adapted GH8 endo-β-1,4-glucanase with high specific activity, which can be exploited as a promising candidate in low-temperature processes including textile and food processes.
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Affiliation(s)
- Do Young Kim
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jonghoon Kim
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Soo Min Byeon
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biological Science, Daejeon University, Daejeon, South Korea
| | - Jeong Hae Gwak
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jong Suk Lee
- Biocenter, Gyeonggido Business and Science Accelerator (GBSA), Suwon, South Korea
| | | | - Ho-Yong Park
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
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Yusof NA, Hashim NHF, Bharudin I. Cold Adaptation Strategies and the Potential of Psychrophilic Enzymes from the Antarctic Yeast, Glaciozyma antarctica PI12. J Fungi (Basel) 2021; 7:jof7070528. [PMID: 34209103 PMCID: PMC8306469 DOI: 10.3390/jof7070528] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/19/2021] [Accepted: 06/25/2021] [Indexed: 12/20/2022] Open
Abstract
Psychrophilic organisms possess several adaptive strategies which allow them to sustain life at low temperatures between −20 to 20 °C. Studies on Antarctic psychrophiles are interesting due to the multiple stressors that exist on the permanently cold continent. These organisms produce, among other peculiarities, cold-active enzymes which not only have tremendous biotechnological potential but are valuable models for fundamental research into protein structure and function. Recent innovations in omics technologies such as genomics, transcriptomics, proteomics and metabolomics have contributed a remarkable perspective of the molecular basis underpinning the mechanisms of cold adaptation. This review critically discusses similar and different strategies of cold adaptation in the obligate psychrophilic yeast, Glaciozyma antarctica PI12 at the molecular (genome structure, proteins and enzymes, gene expression) and physiological (antifreeze proteins, membrane fluidity, stress-related proteins) levels. Our extensive studies on G. antarctica have revealed significant insights towards the innate capacity of- and the adaptation strategies employed by this psychrophilic yeast for life in the persistent cold. Furthermore, several cold-active enzymes and proteins with biotechnological potential are also discussed.
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Affiliation(s)
- Nur Athirah Yusof
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia;
| | - Noor Haza Fazlin Hashim
- Water Quality Laboratory, National Water Research Institute Malaysia (NAHRIM), Ministry of Environment and Water, Jalan Putra Permai, Seri Kembangan 43300, Selangor, Malaysia;
| | - Izwan Bharudin
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
- Correspondence:
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Psychrophilic enzymes: structural adaptation, pharmaceutical and industrial applications. Appl Microbiol Biotechnol 2021; 105:899-907. [PMID: 33427934 DOI: 10.1007/s00253-020-11074-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/11/2020] [Accepted: 12/23/2020] [Indexed: 12/30/2022]
Abstract
Psychrophiles are cold-living microorganisms synthesizing enzymes that are permanently active at almost near-zero temperatures. Psychrozymes are supposed to be structurally more flexible than their homologous proteins. This structural flexibility enables these proteins to undergo conformational changes during catalysis and improve catalytic efficiency at low temperatures. The outstanding characteristics of the psychrophilic enzymes have attracted the attention of the scientific community to utilize them in a wide variety of industrial and pharmaceutical applications. In this review, we first highlight the current knowledge of the cold-adaptation mechanisms of the psychrophiles. In the sequel, we describe the potential applications of the enzymes in different biotechnological processes specifically, in the production of industrial and pharmaceutical products. KEY POINTS: • Methods that organisms have evolved to survive and proliferate at cold environments. • The economic benefits due to their high activity at low and moderate temperatures. • Applications of the psychrophiles in biotechnological and pharmaceutical industry.
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Badur AH, Ammar EM, Yalamanchili G, Hehemann JH, Rao CV. Characterization of the GH16 and GH17 laminarinases from Vibrio breoganii 1C10. Appl Microbiol Biotechnol 2019; 104:161-171. [PMID: 31754764 DOI: 10.1007/s00253-019-10243-0] [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] [Received: 08/21/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
Laminarin is an abundant glucose polymer used as an energy reserve by micro- and macroalgae. Bacteria digest and consume laminarin with laminarinases. Their genomes frequently contain multiple homologs; however, the biological role for this replication remains unclear. We investigated the four laminarinases of glycoside hydrolase families GH16 and GH17 from the marine bacterium Vibrio breoganii 1C10, which can use laminarin as its sole carbon source. All four laminarinases employ an endolytic mechanism and specifically cleave the β-1,3-glycosidic bond. Two primarily produce low-molecular weight laminarin oligomers (DP 3-4) whereas the others primarily produce high-molecular weight oligomers (DP > 8), which suggests that these enzymes sequentially degrade laminarin. The results from this work provide an overview of the laminarinases from a single marine bacterium and also provide insights regarding how multiple laminarinases are used to degrade laminarin.
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Affiliation(s)
- Ahmet H Badur
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Ehab M Ammar
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA.,Genetic Engineering and Biotechnology Research Institute, University of Sadat City, El Sadat City, Egypt
| | - Geethika Yalamanchili
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Jan-Hendrik Hehemann
- MARUM MPG Bridge Group Marine Glycobiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA.
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Parvizpour S, Razmara J, Shamsir MS. Temperature adaptation analysis of a psychrophilic mannanase through structural, functional and molecular dynamics simulation. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1492721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Razmara
- Department of Computer Science, Faculty of Mathematical Sciences, University of Tabriz, Tabriz, Iran
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, Johor, Malaysia
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Parvizpour S, Razmara J, Pourseif MM, Omidi Y. In silico design of a triple-negative breast cancer vaccine by targeting cancer testis antigens. ACTA ACUST UNITED AC 2018; 9:45-56. [PMID: 30788259 PMCID: PMC6378095 DOI: 10.15171/bi.2019.06] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/10/2018] [Accepted: 04/14/2018] [Indexed: 12/14/2022]
Abstract
Introduction: Triple-negative breast cancer (TNBC) is an important subtype of breast cancer, which occurs in the absence of estrogen, progesterone and HER-2 receptors. According to the recent studies, TNBC may be a cancer testis antigen (CTA)-positive tumor, indicating that the CTA-based cancer vaccine can be a treatment option for the patients bearing such tumors. Of these antigens (Ags), the MAGE-A family and NY-ESO-1 as the most immunogenic CTAs are the potentially relevant targets for the development of an immunotherapeutic way of the breast cancer treatment. Methods: In the present study, immunoinformatics approach was used to design a multi-epitope peptide vaccine to combat the TNBC. The vaccine peptide was constructed by the fusion of three crucial components, including the CD8+ cytotoxic T lymphocytes (CTLs) epitopes, helper epitopes and adjuvant. The epitopes were predicted from the MAGE-A and NY-ESO-1 Ags. In addition, the granulocyte-macrophage-colony-stimulating factor (GM-CSF) was used as an adjuvant to promote the CD4+ T cells towards the T-helper for more strong induction of CTL responses. The components were conjugated by proper linkers. Results: The vaccine peptide was examined for different physiochemical characteristics to confirm the safety and immunogenic behavior. Furthermore, the 3D-structure of the vaccine peptide was predicted based on the homology modeling approach using the MODELLER v9.17 program. The vaccine structure was also subjected to the molecular dynamics simulation study for structure refinement. The results verified the immunogenicity and safety profile of the constructed vaccine as well as its capability for stimulating both the cellular and humoral immune responses. Conclusion: Based on our in-silico analyses, the proposed vaccine may be considered for the immunotherapy of TNBC.
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Affiliation(s)
- Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Razmara
- Department of Computer Science, Faculty of Mathematical Sciences, University of Tabriz, Tabriz, Iran
| | - Mohammad M Pourseif
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Parvizpour S, Razmara J, Omidi Y. Breast cancer vaccination comes to age: impacts of bioinformatics. ACTA ACUST UNITED AC 2018; 8:223-235. [PMID: 30211082 PMCID: PMC6128970 DOI: 10.15171/bi.2018.25] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 01/01/2023]
Abstract
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Introduction: Breast cancer, as one of the major causes of cancer death among women, is the central focus of this study. The recent advances in the development and application of computational tools and bioinformatics in the field of immunotherapy of malignancies such as breast cancer have emerged the new dominion of immunoinformatics, and therefore, next generation of immunomedicines .
Methods: Having reviewed the most recent works on the applications of computational tools, we provide comprehensive insights into the breast cancer incidence and its leading causes as well as immunotherapy approaches and the future trends. Furthermore, we discuss the impacts of bioinformatics on different stages of vaccine design for the breast cancer, which can be used to produce much more efficient vaccines through a rationalized time- and cost-effective in silico approaches prior to conducting costly experiments.
Results: The tools can be significantly used for designing the immune system-modulating drugs and vaccines based on in silico approaches prior to in vitro and in vivo experimental evaluations. Application of immunoinformatics in the cancer immunotherapy has shown its success in the pre-clinical models. This success returns back to the impacts of several powerful computational approaches developed during the last decade.
Conclusion: Despite the invention of a number of vaccines for the cancer immunotherapy, more computational and clinical trials are required to design much more efficient vaccines against various malignancies, including breast cancer.
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Affiliation(s)
- Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Razmara
- Department of Computer Science, Faculty of mathematical Sciences, University of Tabriz, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Kashif A, Tran LH, Jang SH, Lee C. Roles of Active-Site Aromatic Residues in Cold Adaptation of Sphingomonas glacialis Esterase EstSP1. ACS OMEGA 2017; 2:8760-8769. [PMID: 31457406 PMCID: PMC6645578 DOI: 10.1021/acsomega.7b01435] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/23/2017] [Indexed: 06/10/2023]
Abstract
The aromatic amino acids, Tyr or Trp, which line the active-site walls of esterases, stabilize the catalytic His loop via hydrogen bonding. A Tyr residue is preferred in extremophilic esterases (psychrophilic or hyperthermophilic esterases), whereas a Trp residue is preferred in moderate-temperature esterases. Here, we provide evidence that Tyr and Trp play distinct roles in cold adaptation of the psychrophilic esterase EstSP1 isolated from an Arctic bacterium Sphingomonas glacialis PAMC 26605. Stern-Volmer plots showed that the mutation of Tyr191 to Ala, Phe, Trp, and His resulted in reduced conformational flexibility of the overall protein structure. Interestingly, the Y191W and Y191H mutants showed increased thermal stability at moderate temperatures. All Tyr191 mutants showed reduced catalytic activity relative to wild-type EstSP1. Our results indicate that Tyr with its phenyl hydroxyl group is favored for increased conformational flexibility and high catalytic activity of EstSP1 at low temperatures at the expense of thermal stability. The results of this study suggest that, in the permanently cold Arctic zone, enzyme activity has been selected for psychrophilic enzymes over thermal stability. The results presented herein provide novel insight into the roles of Tyr and Trp residues for temperature adaptation of enzymes that function at low, moderate, and high temperatures.
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Affiliation(s)
| | | | | | - ChangWoo Lee
- E-mail: . Tel: +82-53-850-6464. Fax: +82-53-850-6469
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12
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Yang LL, Tang SK, Huang Y, Zhi XY. Low Temperature Adaptation Is Not the Opposite Process of High Temperature Adaptation in Terms of Changes in Amino Acid Composition. Genome Biol Evol 2015; 7:3426-33. [PMID: 26614525 PMCID: PMC4700962 DOI: 10.1093/gbe/evv232] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Previous studies focused on psychrophilic adaptation generally have demonstrated that multiple mechanisms work together to increase protein flexibility and activity, as well as to decrease the thermostability of proteins. However, the relationship between high and low temperature adaptations remains unclear. To investigate this issue, we collected the available predicted whole proteome sequences of species with different optimal growth temperatures, and analyzed amino acid variations and substitutional asymmetry in pairs of homologous proteins from related species. We found that changes in amino acid composition associated with low temperature adaptation did not exhibit a coherent opposite trend when compared with changes in amino acid composition associated with high temperature adaptation. This result indicates that during their evolutionary histories the proteome-scale evolutionary patterns associated with prokaryotes exposed to low temperature environments were distinct from the proteome-scale evolutionary patterns associated with prokaryotes exposed to high temperature environments in terms of changes in amino acid composition of the proteins.
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Affiliation(s)
- Ling-Ling Yang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Shu-Kun Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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