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Yan H, Zhu X, Liu Z, Jin S, Liu J, Han Z, Woo J, Meng L, Chi X, Han C, Zhao Y, Tucker ME, Zhao Y, Waheed J, Zhao H. Co-removal and recycling of Ba 2+ and Ca 2+ in hypersaline wastewater based on the microbially induced carbonate precipitation technique: Overlooked Ba 2+ in extracellular and intracellular vaterite. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134923. [PMID: 38889469 DOI: 10.1016/j.jhazmat.2024.134923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/28/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
This study investigates the co-precipitation of calcium and barium ions in hypersaline wastewater under the action of Bacillus licheniformis using microbially induced carbonate precipitation (MICP) technology, as well as the bactericidal properties of the biomineralized product vaterite. The changes in carbonic anhydrase activity, pH, carbonate and bicarbonate concentrations in different biomineralization systems were negatively correlated with variations in metal ion concentrations, while the changes in polysaccharides and protein contents in bacterial extracellular polymers were positively correlated with variations in barium concentrations. In the mixed calcium and barium systems, the harvested minerals were vaterite containing barium. The increasing concentrations of calcium promoted the incorporation and adsorption of barium onto vaterite. The presence of barium significantly increased the contents of O-CO, N-CO, and Ba-O in vaterite. Calcium promoted barium precipitation, but barium inhibited calcium precipitation. After being treated by immobilized bacteria, the concentrations of calcium and barium ions decreased from 400 and 274 to 1.72 and 0 mg/L (GB/T15454-2009 and GB8978-1996). Intracellular minerals were also vaterite containing barium. Extracellular vaterite exhibited bactericidal properties. This research presents a promising technique for simultaneously removing and recycling hazardous heavy metals and calcium in hypersaline wastewater.
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Affiliation(s)
- Huaxiao Yan
- College of Chemical and Biological Engineering, College of Earth Science and Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Xiaofei Zhu
- College of Chemical and Biological Engineering, College of Earth Science and Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Zhiyong Liu
- College of Chemical and Biological Engineering, College of Earth Science and Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Shengping Jin
- College of Chemical and Biological Engineering, College of Earth Science and Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Jilai Liu
- College of Chemical and Biological Engineering, College of Earth Science and Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Zuozhen Han
- College of Chemical and Biological Engineering, College of Earth Science and Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China; Laboratory for Marine Mineral Resources, Center for Isotope Geochemistry and Geochronology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Jusun Woo
- School of Earth and Environmental Sciences, Seoul National University, Seoul, 08826, Korea.
| | - Long Meng
- College of Chemical and Biological Engineering, College of Earth Science and Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Xiangqun Chi
- College of Chemical and Biological Engineering, College of Earth Science and Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Chao Han
- College of Chemical and Biological Engineering, College of Earth Science and Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Yanyang Zhao
- College of Chemical and Biological Engineering, College of Earth Science and Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China
| | - Maurice E Tucker
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK; Cabot Institute, University of Bristol, Cantock's Close, Bristol BS8 1UJ, UK
| | - Yueming Zhao
- Qingdao West Coast New District First High School, Qingdao 266555, China
| | - Junaid Waheed
- University of Azad Jammu and Kashmir, Muzaffarabad, Azad Jammu and Kashmir, 13110, Pakistan
| | - Hui Zhao
- College of Chemical and Biological Engineering, College of Earth Science and Engineering, Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, Shandong University of Science and Technology, Qingdao 266590, China.
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Ye Y, Chen F, Shi M, Wang Y, Xiao X, Wu C. Gel Properties and Protein Structures of Minced Pork Prepared with κ-Carrageenan and Non-Meat Proteins. Gels 2024; 10:305. [PMID: 38786222 PMCID: PMC11120799 DOI: 10.3390/gels10050305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Problems with minced pork include water release and low gel strength. This study aimed to investigate the effect of treatments with κ-carrageenan (κ-CAR), egg white powder (EWP), wheat gluten (WG), soy isolate protein (SPI), and a combination of these treatments on the gel properties and protein structures of minced pork. The cooking loss and trapped water within minced pork increased when additives were incorporated; in particular, the SPI group reached 1.31 ± 0.01% and 91.42 ± 0.20%. The hardness and chewiness of minced pork reached their maximum values (38.91 ± 0.80 N, 14.73 ± 0.41 N) when the WG was added. The κ-CAR/WG-minced pork gel network structure was the densest and most stable, characterized by increased hydrophobic interactions, disulfide bonds in the mince gel, and enthalpy value. The α-helix content with κ-CAR/WG treatment decreased from 27% to 7.8%, transforming into other secondary structures. This suggests that the addition of κ-CAR/WG can be a more effective combination for improving the quality of minced pork.
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Affiliation(s)
- Yang Ye
- School of Biological Engineering, Sichuan University of Science and Engineering, Yibin 644005, China; (Y.Y.); (F.C.); (X.X.); (C.W.)
| | - Fei Chen
- School of Biological Engineering, Sichuan University of Science and Engineering, Yibin 644005, China; (Y.Y.); (F.C.); (X.X.); (C.W.)
| | - Meimei Shi
- Food Fermentation Industry Research and Design Institute of Sichuan Province, Chengdu 610000, China;
| | - Yang Wang
- School of Biological Engineering, Sichuan University of Science and Engineering, Yibin 644005, China; (Y.Y.); (F.C.); (X.X.); (C.W.)
| | - Xia Xiao
- School of Biological Engineering, Sichuan University of Science and Engineering, Yibin 644005, China; (Y.Y.); (F.C.); (X.X.); (C.W.)
| | - Chunmei Wu
- School of Biological Engineering, Sichuan University of Science and Engineering, Yibin 644005, China; (Y.Y.); (F.C.); (X.X.); (C.W.)
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Gao S, Huan F, Wu MX, Ni LN, Gu Y, Liu YX, Han TJ, Liu M, Lai D, Liu GM. Mutation of Disulfide Bond Sites Reduces the Immunoreactivity of Cra a 4 by Changing the Structural Characteristics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38598840 DOI: 10.1021/acs.jafc.4c01120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Sarcoplasmic calcium-binding protein (Cra a 4) from Crassostrea angulata belongs to the EF-hand superfamily, and understanding of its structure-allergenicity relationship is still insufficient. In this study, chemical denaturants were used to destroy the structure of Cra a 4, showing that disruption of the structure reduced its IgG-/IgE-binding activity. To explore which critical amino acid site affects the allergenicity of Cra a 4, the mutants were obtained by site-directed mutations in the disulfide bonds site (C97), conformational epitopes (I105, D114), or Ca2+-binding region (D106, D110) and their IgG-/IgE-binding activity was reduced significantly using serological tests. Notably, C97A had the lowest immunoreactivity. In addition, two conformational epitopes of Cra 4 were verified. Meanwhile, the increase of the α-helical content, surface hydrophobicity, and surface electrostatic potential of C97A affected its allergenicity. Overall, the understanding of the structure-allergenicity relationship of Cra a 4 allowed the development of a hypoallergenic mutant.
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Affiliation(s)
- Shuai Gao
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen 361021, Fujian, China
| | - Fei Huan
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen 361021, Fujian, China
| | - Ming-Xuan Wu
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen 361021, Fujian, China
| | - Ling-Na Ni
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen 361021, Fujian, China
| | - Yi Gu
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen 361021, Fujian, China
| | - Ya-Xin Liu
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen 361021, Fujian, China
| | - Tian-Jiao Han
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen 361021, Fujian, China
| | - Meng Liu
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen 361021, Fujian, China
| | - Dong Lai
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen 361021, Fujian, China
| | - Guang-Ming Liu
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen 361021, Fujian, China
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Munna MMR, Islam MA, Shanta SS, Monty MA. Structural, functional, molecular docking analysis of a hypothetical protein from Talaromyces marneffei and its molecular dynamic simulation: an in-silico approach. J Biomol Struct Dyn 2024:1-20. [PMID: 38345137 DOI: 10.1080/07391102.2024.2314264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/29/2024] [Indexed: 03/01/2024]
Abstract
Telaromyces marneffei (formerly Penicillium marneffei) is an endemic pathogenic fungus in Southern China and Southeast Asia. It can cause disease in patients with travel-related exposure to this organism and high morbidity and mortality in acquired immune deficiency syndrome (AIDS). In this study, we analyzed the structure and function of a hypothetical protein from T. marneffei using several bioinformatics tools and servers to unveil novel pharmacological targets and design a peptide vaccine against specific epitopes. A total of seven functional epitopes were screened on the protein, and 'STGVDMWSV' was the most antigenic, non-allergenic and non-toxic. Molecular docking showed stronger affinity between the CTL epitope 'STGVDMWSV' and the MHC I allele HLA-A*02:01, a higher docking score -234.98 kcal/mol, revealed stable interactions during a 100 ns molecular dynamic simulation. Overall, the results of this study revealed that this hypothetical protein is crucial for comprehending biochemical, physiological pathways and identifying novel therapeutic targets for human health. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Masudur Rahman Munna
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md Ariful Islam
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, PR China
| | - Saima Sajnin Shanta
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Masuma Akter Monty
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, PR China
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5
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Behairy MY, Tawfik NZ, Eid RA, Nasser Binjawhar D, Alshaya DS, Fayad E, Elkhatib WF, Abdallah HY. Mannose-binding lectin gene polymorphism in psoriasis and vitiligo: an observational study and computational analysis. Front Med (Lausanne) 2024; 10:1340703. [PMID: 38404462 PMCID: PMC10885344 DOI: 10.3389/fmed.2023.1340703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 12/28/2023] [Indexed: 02/27/2024] Open
Abstract
Introduction Psoriasis and vitiligo are inflammatory autoimmune skin disorders with remarkable genetic involvement. Mannose-binding lectin (MBL) represents a significant immune molecule with one of its gene variants strongly linked to autoimmune diseases. Therefore, in this study, we investigated the role of the MBL variant, rs1800450, in psoriasis and vitiligo disease susceptibility. Methods The study comprised performing in silico analysis, performing an observational study regarding psoriasis patients, and performing an observational study regarding vitiligo patients. Various in silico tools were used to investigate the impact of the selected mutation on the function, stability, post-translational modifications (PTMs), and secondary structures of the protein. In addition, a total of 489 subjects were enrolled in this study, including their demographic and clinicopathological data. Genotyping analysis was performed using real-time PCR for the single nucleotide polymorphism (SNP) rs1800450 on codon 54 of the MBL gene, utilizing TaqMan genotyping technology. In addition, implications of the studied variant on disease susceptibility and various clinicopathological data were analyzed. Results Computational analysis demonstrated the anticipated effects of the mutation on MBL protein. Furthermore, regarding the observational studies, rs1800450 SNP on codon 54 displayed comparable results in our population relative to global frequencies reported via the 1,000 Genomes Project. This SNP showed no significant association with either psoriasis or vitiligo disease risk in all genetic association models. Furthermore, rs1800450 SNP did not significantly correlate with any of the demographic or clinicopathological features of both psoriasis and vitiligo. Discussion Our findings highlighted that the rs1800450 SNP on the MBL2 gene has no role in the disease susceptibility to autoimmune skin diseases, such as psoriasis and vitiligo, among Egyptian patients. In addition, our analysis advocated the notion of the redundancy of MBL and revealed the lack of significant impact on both psoriasis and vitiligo disorders.
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Affiliation(s)
- Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
| | - Noha Z. Tawfik
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Refaat A. Eid
- Pathology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Dalal Nasser Binjawhar
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Dalal Sulaiman Alshaya
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Walid F. Elkhatib
- Microbiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, African Union Organization St., Abbassia, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, Suez, Egypt
| | - Hoda Y. Abdallah
- Department of Histology and Cell Biology (Genetics Unit), Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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6
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Peracha O. PS4: a next-generation dataset for protein single-sequence secondary structure prediction. Biotechniques 2024; 76:63-70. [PMID: 37997848 DOI: 10.2144/btn-2023-0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023] Open
Abstract
Protein secondary structure prediction is a subproblem of protein folding. A light-weight algorithm capable of accurately predicting secondary structure from only the protein residue sequence could provide useful input for tertiary structure prediction, alleviating the reliance on multiple sequence alignments typically seen in today's best-performing models. Unfortunately, existing datasets for secondary structure prediction are small, creating a bottleneck. We present PS4, a dataset of 18,731 nonredundant protein chains and their respective secondary structure labels. Each chain is identified, and the dataset is nonredundant against other secondary structure datasets commonly seen in the literature. We perform ablation studies by training secondary structure prediction algorithms on the PS4 training set and obtains state-of-the-art accuracy on the CB513 test set in zero shots.
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Affiliation(s)
- Omar Peracha
- Department for Continuing Education, University of Oxford, Rewley House, 1 Wellington Square, Oxford, OX1 2JA, United Kingdom
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7
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Ma TM, Huang RH, Collins VI, Wikström M, Batabyal D. Advancement of microfluidic modulation spectroscopy as a highly sensitive protein characterization technique for the detection of small structural changes. Anal Biochem 2023; 683:115350. [PMID: 37858878 DOI: 10.1016/j.ab.2023.115350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
The higher order structure (HOS) of a protein is vital to its function and activity, making it a critical component in the development of protein-based therapeutics. Characterization of HOS can be performed using various biophysical techniques, but many of these methods have limitations such as low throughput, complicated workflow, narrow concentration range, and low sensitivity. Microfluidic Modulation Spectroscopy (MMS) is an emerging technology that addresses these limitations, offering high sensitivity and automated analysis for protein secondary structure. This study evaluates and compares the different well plate formats and scan modes of two MMS instruments. The newer Apollo system features a high throughput 96-well plate format and sweep scan mode that allows a 50% reduction in sample volume consumption and measurement time compared to the previous system. By measuring two proteins with drastically different secondary structures, the results demonstrated that the measurements were highly repeatable (>99% repeatability by area of overlap) regardless of the well plate formats or the scan modes. The limit of quantitation (LOQ) for determining structural impurity using the sweep scan mode was 3.2% and significantly better than that of FTIR at 23% from previous studies. This work highlighted the advancement of MMS as a highly sensitive technique to detect small changes of protein structures due to aggregation or misfolding.
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Affiliation(s)
- Tianhui Maria Ma
- RedShift BioAnalytics, Inc., Boxborough, MA, 01719, United States
| | - Richard H Huang
- RedShift BioAnalytics, Inc., Boxborough, MA, 01719, United States
| | | | - Mats Wikström
- Amgen Inc., Higher Order Structure, Attribute Sciences, Thousand Oaks, CA, 91320, United States
| | - Dipanwita Batabyal
- Amgen Inc., Higher Order Structure, Attribute Sciences, Thousand Oaks, CA, 91320, United States.
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8
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Ekowati J, Tejo BA, Maulana S, Kusuma WA, Fatriani R, Ramadhanti NS, Norhayati N, Nofianti KA, Sulistyowaty MI, Zubair MS, Yamauchi T, Hamid IS. Potential Utilization of Phenolic Acid Compounds as Anti-Inflammatory Agents through TNF-α Convertase Inhibition Mechanisms: A Network Pharmacology, Docking, and Molecular Dynamics Approach. ACS OMEGA 2023; 8:46851-46868. [PMID: 38107968 PMCID: PMC10720000 DOI: 10.1021/acsomega.3c06450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023]
Abstract
Inflammation is a dysregulated immune response characterized by an excessive release of proinflammatory mediators, such as cytokines and prostanoids, leading to tissue damage and various pathological conditions. Natural compounds, notably phenolic acid phytocompounds from plants, have recently garnered substantial interest as potential therapeutic agents to bolster well-being and combat inflammation recently. Based on previous research, the precise molecular mechanism underlying the anti-inflammatory activity of phenolic acids remains elusive. Therefore, this study aimed to predict the molecular mechanisms underpinning the anti-inflammatory properties of selected phenolic acid phytocompounds through comprehensive network pharmacology, molecular docking, and dynamic simulations. Network pharmacology analysis successfully identified TNF-α convertase as a potential target for anti-inflammatory purposes. Among tested compounds, chlorogenic acid (-6.90 kcal/mol), rosmarinic acid (-6.82 kcal/mol), and ellagic acid (-5.46 kcal/mol) exhibited the strongest binding affinity toward TNF-α convertase. Furthermore, phenolic acid compounds demonstrated molecular binding poses similar to those of the native ligand, indicating their potential as inhibitors of TNF-α convertase. This study provides valuable insights into the molecular mechanisms that drive the anti-inflammatory effects of phenolic compounds, particularly through the suppression of TNF-α production via TNF-α convertase inhibition, thus reinforcing their anti-inflammatory attributes.
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Affiliation(s)
- Juni Ekowati
- Department
of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Bimo Ario Tejo
- Department
of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia
- Department
of Chemistry, Faculty of Science,, Universiti
Putra Malaysia, Serdang 43400, Malaysia
| | - Saipul Maulana
- Magister
Programe Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia
- Department
of Pharmacy, Faculty of Mathematics and Natural Sciences, Tadulako University, Palu 94148, Indonesia
| | - Wisnu Ananta Kusuma
- Department
of Computer Science, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia
- Tropical
Biopharmaca Research Center, IPB University, Bogor 16128, Indonesia
| | - Rizka Fatriani
- Tropical
Biopharmaca Research Center, IPB University, Bogor 16128, Indonesia
| | | | - Norhayati Norhayati
- Magister
Programe Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Kholis Amalia Nofianti
- Department
of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Melanny Ika Sulistyowaty
- Department
of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Muhammad Sulaiman Zubair
- Department
of Pharmacy, Faculty of Mathematics and Natural Sciences, Tadulako University, Palu 94148, Indonesia
| | - Takayasu Yamauchi
- Faculty
of Pharmaceutical Sciences, Hoshi University, Tokyo 142-8501, Japan
| | - Iwan Sahrial Hamid
- Faculty
of Veterinary Medicine,Universitas Airlangga, Surabaya 60115, Indonesia
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9
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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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10
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Behairy MY, Eid RA, Otifi HM, Mohammed HM, Alshehri MA, Asiri A, Aldehri M, Zaki MSA, Darwish KM, Elhady SS, El-Shaer NH, Eldeen MA. Unraveling Extremely Damaging IRAK4 Variants and Their Potential Implications for IRAK4 Inhibitor Efficacy. J Pers Med 2023; 13:1648. [PMID: 38138875 PMCID: PMC10744719 DOI: 10.3390/jpm13121648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/24/2023] Open
Abstract
Interleukin-1-receptor-associated kinase 4 (IRAK4) possesses a crucial function in the toll-like receptor (TLR) signaling pathway, and the dysfunction of this molecule could lead to various infectious and immune-related diseases in addition to cancers. IRAK4 genetic variants have been linked to various types of diseases. Therefore, we conducted a comprehensive analysis to recognize the missense variants with the most damaging impacts on IRAK4 with the employment of diverse bioinformatics tools to study single-nucleotide polymorphisms' effects on function, stability, secondary structures, and 3D structure. The residues' location on the protein domain and their conservation status were investigated as well. Moreover, docking tools along with structural biology were engaged in analyzing the SNPs' effects on one of the developed IRAK4 inhibitors. By analyzing IRAK4 gene SNPs, the analysis distinguished ten variants as the most detrimental missense variants. All variants were situated in highly conserved positions on an important protein domain. L318S and L318F mutations were linked to changes in IRAK4 secondary structures. Eight SNPs were revealed to have a decreasing effect on the stability of IRAK4 via both I-Mutant 2.0 and Mu-Pro tools, while Mu-Pro tool identified a decreasing effect for the G198E SNP. In addition, detrimental effects on the 3D structure of IRAK4 were also discovered for the selected variants. Molecular modeling studies highlighted the detrimental impact of these identified SNP mutant residues on the druggability of the IRAK4 ATP-binding site towards the known target inhibitor, HG-12-6, as compared to the native protein. The loss of important ligand residue-wise contacts, altered protein global flexibility, increased steric clashes, and even electronic penalties at the ligand-binding site interfaces were all suggested to be associated with SNP models for hampering the HG-12-6 affinity towards IRAK4 target protein. This given model lays the foundation for the better prediction of various disorders relevant to IRAK4 malfunction and sheds light on the impact of deleterious IRAK4 variants on IRAK4 inhibitor efficacy.
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Affiliation(s)
- Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt;
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (R.A.E.); (H.M.O.)
| | - Hassan M. Otifi
- Department of Pathology, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (R.A.E.); (H.M.O.)
| | - Heitham M. Mohammed
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Mohammed A. Alshehri
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia; (M.A.A.)
| | - Ashwag Asiri
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia; (M.A.A.)
| | - Majed Aldehri
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Mohamed Samir A. Zaki
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Nahla H. El-Shaer
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig 44511, Egypt;
| | - Muhammad Alaa Eldeen
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig 44511, Egypt;
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11
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Zhang T, Wu Z, Ng G, Boyer C. Design of an Oxygen-Tolerant Photo-RAFT System for Protein-Polymer Conjugation Achieving High Bioactivity. Angew Chem Int Ed Engl 2023; 62:e202309582. [PMID: 37591792 DOI: 10.1002/anie.202309582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/19/2023]
Abstract
Protein-polymer conjugates have significant potential in pharmaceutical and biomedical applications. To enable their widespread use, robust conjugation techniques are crucial. This study introduces a photo-initiated reversible addition-fragmentation chain-transfer (Photo-RAFT) polymerization system that exhibits excellent oxygen tolerance. This system allows for the synthesis of protein-polymer conjugates with high bioactivity under mild and aerobic conditions. Three photocatalytic systems utilizing Eosin Y (EY) as the photocatalyst with two different cocatalysts (ascorbic acid and triethanolamine) were investigated, each generating distinct reactive oxygen species (ROS) such as singlet oxygen, superoxide, hydrogen peroxide, and hydroxyl radicals. The impact of these ROS on three model proteins (lysozyme, albumin, and myoglobin) was evaluated, demonstrating varying bioactivities based on the ROS produced. The EY/TEOA system was identified as the optimal photo-RAFT initiating system, enabling the preparation of protein-polymer conjugates under aerobic conditions while maintaining high protein enzymatic activity. To showcase the potential of this approach, lysozyme-poly(dimethylaminoethyl acrylate) conjugates were successfully prepared and exhibited enhanced antimicrobial property against Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Tong Zhang
- Cluster for Advanced Macromolecular Design and UNSW RNA Institute, School of Chemical Engineering, The University of New South Wales, 2052, Sydney, NSW, Australia
| | - Zilong Wu
- Cluster for Advanced Macromolecular Design and UNSW RNA Institute, School of Chemical Engineering, The University of New South Wales, 2052, Sydney, NSW, Australia
| | - Gervase Ng
- Cluster for Advanced Macromolecular Design and UNSW RNA Institute, School of Chemical Engineering, The University of New South Wales, 2052, Sydney, NSW, Australia
| | - Cyrille Boyer
- Cluster for Advanced Macromolecular Design and UNSW RNA Institute, School of Chemical Engineering, The University of New South Wales, 2052, Sydney, NSW, Australia
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Ahmad S, Nazarian S, Alizadeh A, Pashapour Hajialilou M, Tahmasebian S, Alharbi M, Alasmari AF, Shojaeian A, Ghatrehsamani M, Irfan M, Pazoki-Toroudi H, Sanami S. Computational design of a multi-epitope vaccine candidate against Langya henipavirus using surface proteins. J Biomol Struct Dyn 2023:1-18. [PMID: 37713338 DOI: 10.1080/07391102.2023.2258403] [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: 05/15/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
In July 2022, Langya henipavirus (LayV) was identified in febrile patients in China. There is currently no approved vaccine against this virus. Therefore, this research aimed to design a multi-epitope vaccine against LayV using reverse vaccinology. The best epitopes were selected from LayV's fusion protein (F) and glycoprotein (G), and a multi-epitope vaccine was designed using these epitopes, adjuvant, and appropriate linkers. The physicochemical properties, antigenicity, allergenicity, toxicity, and solubility of the vaccine were evaluated. The vaccine's secondary and 3D structures were predicted, and molecular docking and molecular dynamics (MD) simulations were used to assess the vaccine's interaction and stability with toll-like receptor 4 (TLR4). Immune simulation, codon optimization, and in silico cloning of the vaccine were also performed. The vaccine candidate showed good physicochemical properties, as well as being antigenic, non-allergenic, and non-toxic, with acceptable solubility. Molecular docking and MD simulation revealed that the vaccine and TLR4 have stable interactions. Furthermore, immunological simulation of the vaccine indicated its ability to elicit immune responses against LayV. The vaccine's increased expression was also ensured using codon optimization. This study's findings were encouraging, but in vitro and in vivo tests are needed to confirm the vaccine's protective effect.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
- Department of Computer Sciences, Virginia Tech, Blacksburg, VA, USA
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Shahin Nazarian
- Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA
| | - Akram Alizadeh
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Maryam Pashapour Hajialilou
- School of Metallurgy and Materials Engineering, Iran University of Science and Technology (IUST), Tehran, Iran
| | - Shahram Tahmasebian
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ali Shojaeian
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mahdi Ghatrehsamani
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Physiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Sanami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
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13
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Rajendran Krishnamoorthy H, Karuppasamy R. Designing a novel SOX9 based multi-epitope vaccine to combat metastatic triple-negative breast cancer using immunoinformatics approach. Mol Divers 2023; 27:1829-1842. [PMID: 36214961 PMCID: PMC9549049 DOI: 10.1007/s11030-022-10539-w] [Citation(s) in RCA: 5] [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: 08/29/2022] [Accepted: 09/28/2022] [Indexed: 11/27/2022]
Abstract
Immunotherapies are a promising treatment option especially for the management of TNBC owing to its higher levels of tumour-associated antigens together with higher mutational load. Of note, the administration of preventive vaccines in the early stage of the cancer holds promise for effective disease management. Therefore, the present study aimed to develop a novel multi-epitope peptide-based vaccination against TNBC employing SOX9, which has recently been recognized as a key regulator of TNBC metastasis. The immunodominant regions from the SOX9 protein were computed and assessed based on their ability to elicit both T and B lymphocyte mediated responses. The resultant epitopes were fused using appropriate linkers (EAAAK, KK, AAY and GPGPG) and adjuvant (50S ribosomal protein L7/L12) to enhance the vaccine's immunogenicity. The physicochemical properties and population coverage were also anticipated for the constructed vaccine. Adding together, docking and dynamics simulation studies were performed on the modelled vaccine against TLR-4 to provide insight into the stability. Finally, the designed vaccine was cloned into the pET28 (+) vector and immunological simulation studies were carried out. These results demonstrate that our designed vaccine had the potency to trigger humoral and cellular immune responses. Based on these collective evidences, the final proposed vaccine could be an interesting therapeutics for the management of TNBC in the near future. Schematic representation of an efficient vaccine design framework by combining the range of immunoinformatics strategies.
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Affiliation(s)
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
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14
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Behairy MY, Soltan MA, Eldeen MA, Abdulhakim JA, Alnoman MM, Abdel-Daim MM, Otifi H, Al-Qahtani SM, Zaki MSA, Alsharif G, Albogami S, Jafri I, Fayad E, Darwish KM, Elhady SS, Eid RA. HBD-2 variants and SARS-CoV-2: New insights into inter-individual susceptibility. Front Immunol 2022; 13:1008463. [PMID: 36569842 PMCID: PMC9780532 DOI: 10.3389/fimmu.2022.1008463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Background A deep understanding of the causes of liability to SARS-CoV-2 is essential to develop new diagnostic tests and therapeutics against this serious virus in order to overcome this pandemic completely. In the light of the discovered role of antimicrobial peptides [such as human b-defensin-2 (hBD-2) and cathelicidin LL-37] in the defense against SARS-CoV-2, it became important to identify the damaging missense mutations in the genes of these molecules and study their role in the pathogenesis of COVID-19. Methods We conducted a comprehensive analysis with multiple in silico approaches to identify the damaging missense SNPs for hBD-2 and LL-37; moreover, we applied docking methods and molecular dynamics analysis to study the impact of the filtered mutations. Results The comprehensive analysis reveals the presence of three damaging SNPs in hBD-2; these SNPs were predicted to decrease the stability of hBD-2 with a damaging impact on hBD-2 structure as well. G51D and C53G mutations were located in highly conserved positions and were associated with differences in the secondary structures of hBD-2. Docking-coupled molecular dynamics simulation analysis revealed compromised binding affinity for hBD-2 SNPs towards the SARS-CoV-2 spike domain. Different protein-protein binding profiles for hBD-2 SNPs, in relation to their native form, were guided through residue-wise levels and differential adopted conformation/orientation. Conclusions The presented model paves the way for identifying patients prone to COVID-19 in a way that would guide the personalization of both the diagnostic and management protocols for this serious disease.
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Affiliation(s)
- Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt,*Correspondence: Mohamed A Soltan, ; Mohammed Y. Behairy,
| | - Mohamed A. Soltan
- Department of Microbiology and immunology, Faculty of Pharmacy, Sinai University – Kantara Branch, Ismailia, Egypt,*Correspondence: Mohamed A Soltan, ; Mohammed Y. Behairy,
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Biology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Jawaher A. Abdulhakim
- Medical Laboratory Department, College of Applied Medical Sciences, Taibah University, Yanbu, Saudi Arabia
| | - Maryam M. Alnoman
- Biology Department, Faculty of Science, Taibah University, Yanbu, Saudi Arabia
| | - Mohamed M. Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, Jeddah, Saudi Arabia,Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Hassan Otifi
- Pathology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Saleh M. Al-Qahtani
- Department of Child Health, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Mohamed Samir A. Zaki
- Anatomy Department, College of Medicine, King Khalid University, Abha, Saudi Arabia,Department of Histology and Cell Biology, College of Medicine, Zagazig University, Zagazig, Egypt
| | - Ghadi Alsharif
- College of Clinical Laboratory Sciences, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Sarah Albogami
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Ibrahim Jafri
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Refaat A. Eid
- Pathology Department, College of Medicine, King Khalid University, Abha, Saudi Arabia
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15
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Ahanger IA, Parray ZA, Raina N, Bashir S, Ahmad F, Hassan MI, Shahid M, Sharma A, Islam A. Counteraction of the cetyltrimethylammonium bromide-induced protein aggregation by Heparin: Potential impact on protein aggregation and neurodegenerative diseases using biophysical approaches. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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16
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Dingle K, Novev JK, Ahnert SE, Louis AA. Predicting phenotype transition probabilities via conditional algorithmic probability approximations. J R Soc Interface 2022; 19:20220694. [PMID: 36514888 PMCID: PMC9748496 DOI: 10.1098/rsif.2022.0694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Unravelling the structure of genotype-phenotype (GP) maps is an important problem in biology. Recently, arguments inspired by algorithmic information theory (AIT) and Kolmogorov complexity have been invoked to uncover simplicity bias in GP maps, an exponentially decaying upper bound in phenotype probability with the increasing phenotype descriptional complexity. This means that phenotypes with many genotypes assigned via the GP map must be simple, while complex phenotypes must have few genotypes assigned. Here, we use similar arguments to bound the probability P(x → y) that phenotype x, upon random genetic mutation, transitions to phenotype y. The bound is [Formula: see text], where [Formula: see text] is the estimated conditional complexity of y given x, quantifying how much extra information is required to make y given access to x. This upper bound is related to the conditional form of algorithmic probability from AIT. We demonstrate the practical applicability of our derived bound by predicting phenotype transition probabilities (and other related quantities) in simulations of RNA and protein secondary structures. Our work contributes to a general mathematical understanding of GP maps and may facilitate the prediction of transition probabilities directly from examining phenotype themselves, without utilizing detailed knowledge of the GP map.
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Affiliation(s)
- Kamaludin Dingle
- Department of Chemical Engineering and Biotechnology, Cambridge University, Cambridge CB2 1TN, UK,Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA,Department of Mathematics and Natural Sciences, Centre for Applied Mathematics and Bioinformatics (CAMB), Gulf University for Science and Technology, 32093, Kuwait
| | - Javor K. Novev
- Department of Chemical Engineering and Biotechnology, Cambridge University, Cambridge CB2 1TN, UK
| | - Sebastian E. Ahnert
- Department of Chemical Engineering and Biotechnology, Cambridge University, Cambridge CB2 1TN, UK
| | - Ard A. Louis
- Department of Physics, Rudolf Peierls Centre for Theoretical Physics, Oxford University, Oxford OX1 2JD, UK
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17
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Gupta N, Khan MA, Capasso G, Zacchia M. Computational and Structural Analysis to Assess the Pathogenicity of Bardet-Biedl Syndrome Related Missense Variants Identified in Bardet-Biedl Syndrome 10 Gene (BBS10). ACS OMEGA 2022; 7:37654-37662. [PMID: 36312387 PMCID: PMC9608418 DOI: 10.1021/acsomega.2c04522] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/28/2022] [Indexed: 05/27/2023]
Abstract
Bardet-Biedl Syndrome (BBS) is a rare inherited disorder resulting in multiple organ dysfunctions, whose cardinal clinical features include cognitive impairment, obesity, and renal dysfunction. Although it is highly heterogeneous at genetic levels, BBS10 is one of the major causative genes worldwide. The BBS10 protein is part of a multiprotein complex localized at the basal body of the primary cilium. With the advancement of sequencing technologies, novel missense mutations are regularly reported in BBS10. However, prioritizing missense variants and conducting further in-depth analysis are key challenges in addressing their pathogenic effect. This study aims to characterize the known missense mutations of BBS10 by combining nine different in silico tools (SIFT, SNAP2, PROVEAN, Align-GVGD, ConSurf, I Mutant, MuPro, PremPS, and Dynamut) and molecular dynamics (MD) simulations. A total of 101 BBS10 missense variants have been analyzed. Our results showed that six BBS10 missense variants (Ser191Leu, Cys19Gly, Ile342Thr, Cys371Ser, Ala417Glu, and Tyr613Cys) were potentially deleterious. Overall, this study provides a comprehensive workflow for screening BBS10 missense mutations to identify pathogenic variants effectively.
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Affiliation(s)
- Neha Gupta
- Unit
of Nephrology, Department of Translational Medical Sciences, University of Campania, L. Vanvitelli, Via Leonardo Bianchi, 80131 Naples, Italy
- BioGem
S.C.A.R.L., Contrada Camporeale, 83031 Ariano Irpino
AV, Italy
| | - Mudassar Ali Khan
- Advanced
Centre for Treatment, Research and Education
in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India
- Homi
Bhabha National Institute, Training School
Complex, Anushaktinagar, Mumbai 400094, India
| | - Giovambattista Capasso
- Unit
of Nephrology, Department of Translational Medical Sciences, University of Campania, L. Vanvitelli, Via Leonardo Bianchi, 80131 Naples, Italy
- BioGem
S.C.A.R.L., Contrada Camporeale, 83031 Ariano Irpino
AV, Italy
| | - Miriam Zacchia
- Unit
of Nephrology, Department of Translational Medical Sciences, University of Campania, L. Vanvitelli, Via Leonardo Bianchi, 80131 Naples, Italy
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Antiviral phytocompounds “ellagic acid” and “(+)-sesamin” of Bridelia retusa identified as potential inhibitors of SARS-CoV-2 3CL pro using extensive molecular docking, molecular dynamics simulation studies, binding free energy calculations, and bioactivity prediction. Struct Chem 2022; 33:1445-1465. [PMID: 35571865 PMCID: PMC9086128 DOI: 10.1007/s11224-022-01959-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/28/2022] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected billions and has killed millions to date. Studies are being carried out to find therapeutic molecules that can potentially inhibit the replication of SARS-CoV-2. 3-chymotrypsin-like protease (3CL pro) involved in the polyprotein cleavage process is believed to be the key target for viral replication, and hence is an attractive target for the discovery of antiviral molecules. In the present study, we aimed to identify natural phytocompounds from Bridelia retusa as potential inhibitors of SARS-CoV-2 3CL pro (PDB ID: 6M2N) using in silico techniques. Molecular docking studies conducted with three different tools in triplicates revealed that ellagic acid (BR6) and (+)-sesamin (BR13) has better binding affinity than the co-crystal inhibitor “3WL” of 6M2N. BR6 and BR13 were found to have a high LD50 value with good bioavailability. 3WL, BR6, and BR13 bind to the same active binding site and interacted with the HIS41-CYS145 catalytic dyad including other crucial amino acids. Molecular dynamics simulation studies revealed stability of protein–ligand complexes as evidenced from root-mean-square deviations, root-mean-square fluctuations (RMSF), protein secondary structure elements, ligand-RMSF, protein–ligand contacts, ligand torsions, and ligand properties. BR6 (−22.3064 kcal/mol) and BR13 (−19.1274 kcal/mol) showed a low binding free energy value. The Bayesian statistical model revealed BR6 and BR13 as better protease inhibitors than 3WL. Moreover, BR6 and BR13 had already been reported to elicit antiviral activities. Therefore, we conclude that ellagic acid and (+)-sesamin as natural antiviral phytocompounds with inhibitory potential against SARS-CoV-2 3CL pro.
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Behairy MY, Abdelrahman ALA, Abdallah HY, Ibrahim EEDA, Sayed AA, Azab MM. In silico analysis of missense variants of the C1qA gene related to infection and autoimmune diseases. J Taibah Univ Med Sci 2022; 17:1074-1082. [PMID: 36212588 PMCID: PMC9519598 DOI: 10.1016/j.jtumed.2022.04.014] [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: 12/30/2021] [Revised: 02/28/2022] [Accepted: 04/28/2022] [Indexed: 11/15/2022] Open
Abstract
Objectives C1q is a key activator of the classical pathway of the complement system and exerts consequences relating to opsonization and phagocytosis. The C1qA gene is one of three genes encoding the C1q molecule. Defects in C1q, and especially in C1qA, have been linked to an increased susceptibility to infection, sepsis, and systemic lupus erythematosus. These defects could arise from missense single nucleotide polymorphisms (SNPs) and their deleterious impacts on protein structure and function. Thus, identifying high-risk missense SNPs in C1qA has become a necessity if we are to identify appropriate measures for prevention and management of affected patients. Methods A comprehensive in silico study was conducted to screen the 184 missense SNPs in the C1qA gene using different tools with different algorithms and approaches. We investigated the impact of SNPs on protein function, stability, and structure. In addition, we identified the location of the SNPs on protein domains, secondary structure alignment, and the phylogenetic conservation of their positions. Results Of the 184 missense SNPs, 10 SNPs were predicted to be the most damaging to protein function and structure. Conclusion Ten missense SNPs were predicted to have the highest risk of damaging protein function and structure, thus leading to infection, sepsis, and systemic lupus erythematosus. These 10 SNPs constitute the best candidates for further experimental investigations.
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20
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Yang YF, Zhao XH. Structure and property changes of whey protein isolate in response to the chemical modification mediated by horseradish peroxidase, glucose oxidase and d-glucose. Food Chem 2022; 373:131328. [PMID: 34700037 DOI: 10.1016/j.foodchem.2021.131328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/25/2021] [Accepted: 10/02/2021] [Indexed: 11/19/2022]
Abstract
Whey protein isolate (WPI) was modified by a ternary system containing horseradish peroxidase, glucose oxidase and d-glucose through the one- and two-step protocols, yielding two respective crosslinked products MWPI-1 and MWPI-2 with the enhanced relative dityrosine contents (127.4 and 101.0). Compared with WPI, both MWPI-1 and MWPI-2 had much ordered secondary structure, increased disulfide-bond contents, average particle sizes, surface hydrophobicity, oil-binding capacity, emulsification and thermal stability, but reduced free sulfhydryl groups contents and in vitro digestibility. Moreover, both MWPI-1 and MWPI-2 in dispersions showed higher apparent viscosity, larger viscoelastic moduli than WPI, together with the lower gelling temperatures (67.1 °C and 70.1 °C versus 73.6 °C). Overall, MWPI-1 with a higher crosslinking extent consistently exhibited more remarkable property alteration. It is concluded that the ternary system is an effective approach when aiming to modify secondary structure especially these properties of WPI, such as aggregation, emulsification, gelation, rheology and thermal stability.
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Affiliation(s)
- Yu-Fei Yang
- School of Biology and Food Engineering, Guangdong University of Petrochemical Technology, 525000 Maoming, Guangdong, PR China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122 Wuxi, Jiangsu, PR China
| | - Xin-Huai Zhao
- School of Biology and Food Engineering, Guangdong University of Petrochemical Technology, 525000 Maoming, Guangdong, PR China; Research Centre of Food Nutrition and Human Healthcare, Guangdong University of Petrochemical Technology, 525000 Maoming, Guangdong, PR China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong University of Petrochemical Technology, 525000 Maoming, Guangdong, PR China.
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Day K, Schneible JD, Young AT, Pozdin VA, Van Den Driessche G, Gaffney LA, Prodromou R, Freytes DO, Fourches D, Daniele M, Menegatti S. Photoinduced reconfiguration to control the protein-binding affinity of azobenzene-cyclized peptides. J Mater Chem B 2021; 8:7413-7427. [PMID: 32661544 DOI: 10.1039/d0tb01189d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The impact of next-generation biorecognition elements (ligands) will be determined by the ability to remotely control their binding activity for a target biomolecule in complex environments. Compared to conventional mechanisms for regulating binding affinity (pH, ionic strength, or chaotropic agents), light provides higher accuracy and rapidity, and is particularly suited for labile targets. In this study, we demonstrate a general method to develop azobenzene-cyclized peptide ligands with light-controlled affinity for target proteins. Light triggers a cis/trans isomerization of the azobenzene, which results in a major structural rearrangement of the cyclic peptide from a non-binding to a binding configuration. Critical to this goal are the ability to achieve efficient photo-isomerization under low light dosage and the temporal stability of both cis and trans isomers. We demonstrated our method by designing photo-switchable peptides targeting vascular cell adhesion marker 1 (VCAM1), a cell marker implicated in stem cell function. Starting from a known VCAM1-binding linear peptide, an ensemble of azobenzene-cyclized variants with selective light-controlled binding were identified by combining in silico design with experimental characterization via spectroscopy and surface plasmon resonance. Variant cycloAZOB[G-VHAKQHRN-K] featured rapid, light-controlled binding of VCAM1 (KD,trans/KD,cis ∼ 130). Biotin-cycloAZOB[G-VHAKQHRN-K] was utilized to label brain microvascular endothelial cells (BMECs), showing co-localization with anti-VCAM1 antibodies in cis configuration and negligible binding in trans configuration.
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Affiliation(s)
- Kevin Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina, USA.
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Filiz E, Aydın Akbudak M. Investigation of PIC1 (permease in chloroplasts 1) gene’s role in iron homeostasis: bioinformatics and expression analyses in tomato and sorghum. Biometals 2019; 33:29-44. [DOI: 10.1007/s10534-019-00228-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 11/28/2019] [Indexed: 11/28/2022]
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Molecular characterization and computational structure prediction of activin receptor type IIB in aseel and broiler chicken. Res Vet Sci 2019; 126:139-149. [PMID: 31491670 DOI: 10.1016/j.rvsc.2019.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/19/2019] [Accepted: 08/27/2019] [Indexed: 11/20/2022]
Abstract
The present study was formulated to characterize and comprehend the molecular structural characteristics of ACTRIIB receptor in Aseel and control broiler (CB) populations. The full length coding sequence (1539 bp) of the receptor was amplified, cloned, sequenced and analyzed using bioinformatic tools. The physico chemical properties of protein and structural features like secondary structure, solvent accessibility and disorder regions were computed. The 3D structure was predicted by I-TASSER and evaluated by Ramachandran Plot and tools under Structural Analysis and Verification Server. The nucleotides differences between CB and Aseel were c. [156G > A; 210 T > C; 493C > T; c.520G > C; 665A > C; 686G > A; 937C > G; 1011A > C; 1130A > G; 1208 T > A; 1326 T > C; 1433 T > C]. The amino acid substitutions between CB and Aseel were p. [(Pro165Ser; Glu174Gln; Gln222Pro; Ser229Asn; His313Asp; Gln377Arg; Val403Asp; and Ile478Thr)]. While, the silent changes includes p. [(Lys53=; Glu71=; Leu337=; Asp442=)]. The molecular weight of mature protein was predicted to be 55.51 kDa and 57.80 kDa in Aseel and CB, respectively. The higher rank 3D model had a C-score of -1.60 in Aseel and - 1.41 in CB, while the estimated TM-score (0.54 ± 0.14) and RMSD (5.8 ± 1.2 Å) were found to be similar in Aseel and CB. Among the 512 residues, >90% were in favored region, 4.7% in allowed region and <1.5% in disallowed region in both Aseel and CB. The pattern of contact map was comparable in Aseel and CB. The Hydrogen bond plots of the Aseel and CB shared similar secondary structure pattern. The ACTRIIB protein was predicted to interact with ACVR1B, ACVR1C, INHBA, SMAD 1,2,5,7 & 9 and BMPR1A&B. Clustal and phylogenetic analysis implied that both the lines were closely related and formed a sub cluster with in avian cluster. The current research provides insights about structural and functional aspects of the receptor and also aids in understanding the evolutionary history of ACTRIIB.
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Bandyopadhyay AK, Islam RNU, Mitra D, Banerjee S, Goswami A. Analysis of salt-bridges in prolyl oligopeptidase from Pyrococcus furiosus and Homo sapiens. Bioinformation 2019; 15:214-225. [PMID: 31354198 PMCID: PMC6637400 DOI: 10.6026/97320630015214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/09/2019] [Accepted: 03/11/2019] [Indexed: 01/19/2023] Open
Abstract
Hyper thermophilic archaea not only tolerate high temperature but also operate its biochemical machineries, normally under these conditions. However, the structural signatures in proteins that answer for the hyper thermo-stability relative to its mesophilic homologue remains poorly understood. We present comparative analyses of sequences, structures and salt-bridges of prolyl-oligopeptidase from Pyrococcus furiosus (pfPOP - PDB ID: 5T88) and human (huPOP - PDB ID: 3DDU). A similar level of hydrophobic and hydrophilic residues in pfPOP and huPOP is observed. A low level of interactions between shell-waters and atom-types in pfPOP indicated hyper thermophilic features are negligible. Salt-bridge-forming-residues (sbfrs) are high in pfPOP's core and surface (pfPOP). Increased sbfrs largely indicate specific-electrostatic is important for thermo stability in pfPOP. Four classes of sbfrs are found namely positionally non-conservative (PNCS), conservative (PCS), unchanged (PU) and interchanged (PIC) type of substitutions. PNCS-sbfrs constitutes 28% and it is associated with the topology of pfPOP at high temperature. PCS helps to increase the salt-bridge population. It is also found that PU maintains similar salt-bridges at the active site and other binding sites while PIC abolishes mesophilic patterns.
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Affiliation(s)
| | | | - Debanjan Mitra
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
| | - Sahini Banerjee
- Department of Biological Sciences, ISI, Kolkata, West Bengal, India
| | - Arunava Goswami
- Department of Biological Sciences, ISI, Kolkata, West Bengal, India
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Ibrahim MAA, Hassan AMA. Comparative Modeling and Evaluation of Leukotriene B4 Receptors for Selective Drug Discovery Towards the Treatment of Inflammatory Diseases. Protein J 2019; 37:518-530. [PMID: 30267300 DOI: 10.1007/s10930-018-9797-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Leukotriene B4 (LTB4) exerts its biological effects through stimulation of specific G protein-coupled receptors (GPCRs)-namely BLT1 and BLT2. Due to the absence of human BLT1 and BLT2 crystal structures, the current study was set to predict the 3D structures of these two receptors for structure-based anti-inflammatory drug discovery. Homology modeling of the BLT1 receptor was first constructed, based on various X-ray and NMR GPCR templates, followed by molecular dynamics (MD) refinement. Using a single-template approach, nine well-established alignment methods and ten secondary structure prediction methods during the backbone generation were implemented and assessed. The binding sites of the BLT1 receptor were then mapped using fifteen chemical probes with the help of FTMAP and AutoDock Vina 4.2 software. Model validation was performed through the docking of eight specific antagonists that have experimental inhibition constants (ki) towards BLT1. The antagonists-BLT1 docked structures were then subjected to AMBER-based molecular mechanical minimization and the corresponding binding energies were calculated using molecular mechanics-generalized Born surface area (MM/GBSA) approach. According to the results, the most energetically stable models were constructed using SAlign method for the alignment process and PSIPRED for secondary structure prediction. In comparison, the refined BLT1 model built on 2KS9 as an NMR template has the lowest DOPE energy compared to those built on 4EA3 and 4XT1 as X-ray templates. According to the mapping results, two main binding sites were identified: one was among TMs II, III and VII and the other was among TMs III, IV and V. For the antagonists, correlation between binding energies and experimental data was in a good agreement, with a correlation coefficient (R2 value) of 0.91. Due to the great amino acid sequence similarity between BLT1 and BLT2 receptors (calculated as 45.2%), BLT2 model was constructed based on the predicted BLT1 model.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt.
| | - Alaa M A Hassan
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
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Akbudak MA, Filiz E, Kontbay K. DREB2 (dehydration-responsive element-binding protein 2) type transcription factor in sorghum ( Sorghum bicolor): genome-wide identification, characterization and expression profiles under cadmium and salt stresses. 3 Biotech 2018; 8:426. [PMID: 30305995 DOI: 10.1007/s13205-018-1454-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022] Open
Abstract
Biotic and abiotic stresses negatively affect fitness, biomass production, and crop yield in plants. The dehydration-responsive element-binding proteins (DREB) are important transcription factors (TFs), and are induced by abiotic and biotic stresses. In this study, genome-wide identification, in silico sequence, and phylogenetic analyses and expression analyses of DREB2 genes under cadmium (Cd) and salt (NaCl) stresses in sorghum (Sorghum bicolor, Sb) were performed. Six putative SbDREB2 genes were identified in sorghum genome and all contained AP2 domain (PF00847). Nucleotide diversities in SbDREB2 genes were calculated as π: 0.53 and θ: 0.39, respectively. While exon numbers of them were either one or two, length of SbDREB2 proteins ranged from 238 to 388 amino acid residues. Fifty-six cis-acting regulatory elements, which are tissue specific, light, hormone, and stress responsive, were identified in the promotor regions of SbDREB2 genes. Analyses on digital expression data indicated that SbDREB2A and SbDREB2B are more expressed genes than other SbDREB genes in sorghum. Under Cd and NaCl stresses, expressions of SbDREB2 genes were induced at different levels. All SbDREB2 genes in root were up-regulated under salt stress. In case of Cd stress, SbDREB2D gene was particularly up-regulated in leaves and roots. Co-expression analyses revealed four of TFs in co-expression network, indicating that they have roles in transcriptional cascade. Furthermore, five miRNA target regions were identified for four SbDREB2 genes, indicating their roles in post-transcriptional regulation. The predicted 3D structure of SbDREB2 proteins showed some structural divergences and structure overlap between rice and sorghum varied at between 26.58 and 50%. Finally, obtained data could be used in breeding of stress-tolerant plants, particularly genetically engineered DREB2 expressing plants. Findings in this study would also contribute to the understanding of DREB2 genes in plants, especially in sorghum.
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Chordia N, Lakhawat K, Kumar A. Identification of Drug Target Properties and its validation on Helicobacter pylori. CANADIAN JOURNAL OF BIOTECHNOLOGY 2017. [DOI: 10.24870/cjb.2017-000101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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28
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Mirza SB, Ekhteiari Salmas R, Fatmi MQ, Durdagi S. Discovery of Klotho peptide antagonists against Wnt3 and Wnt3a target proteins using combination of protein engineering, protein-protein docking, peptide docking and molecular dynamics simulations. J Enzyme Inhib Med Chem 2016; 32:84-98. [PMID: 27766889 PMCID: PMC6009926 DOI: 10.1080/14756366.2016.1235569] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The Klotho is known as lifespan enhancing protein involved in antagonizing the effect of Wnt proteins. Wnt proteins are stem cell regulators, and uninterrupted exposure of Wnt proteins to the cell can cause stem and progenitor cell senescence, which may lead to aging. Keeping in mind the importance of Klotho in Wnt signaling, in silico approaches have been applied to study the important interactions between Klotho and Wnt3 and Wnt3a (wingless-type mouse mammary tumor virus (MMTV) integration site family members 3 and 3a). The main aim of the study is to identify important residues of the Klotho that help in designing peptides which can act as Wnt antagonists. For this aim, a protein engineering study is performed for Klotho, Wnt3 and Wnt3a. During the theoretical analysis of homology models, unexpected role of number of disulfide bonds and secondary structure elements has been witnessed in case of Wnt3 and Wnt3a proteins. Different in silico experiments were carried out to observe the effect of correct number of disulfide bonds on 3D protein models. For this aim, total of 10 molecular dynamics (MD) simulations were carried out for each system. Based on the protein–protein docking simulations of selected protein models of Klotho with Wnt3 and Wnt3a, different peptides derived from Klotho have been designed. Wnt3 and Wnt3a proteins have three important domains: Index finger, N-terminal domain and a patch of ∼10 residues on the solvent exposed surface of palm domain. Protein–peptide docking of designed peptides of Klotho against three important domains of palmitoylated Wnt3 and Wnt3a yields encouraging results and leads better understanding of the Wnt protein inhibition by proposed Klotho peptides. Further in vitro studies can be carried out to verify effects of novel designed peptides as Wnt antagonists.
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Affiliation(s)
- Shaher Bano Mirza
- a Department of Biophysics, School of Medicine , Bahcesehir University (BAU) , Istanbul , Turkey.,b Department of Biosciences , COMSATS Institute of Information Technology (CIIT) , Islamabad , Pakistan
| | - Ramin Ekhteiari Salmas
- a Department of Biophysics, School of Medicine , Bahcesehir University (BAU) , Istanbul , Turkey
| | - M Qaiser Fatmi
- b Department of Biosciences , COMSATS Institute of Information Technology (CIIT) , Islamabad , Pakistan
| | - Serdar Durdagi
- a Department of Biophysics, School of Medicine , Bahcesehir University (BAU) , Istanbul , Turkey
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